Several pieces of info have combined to create confusion.
First, speed measurement. All common fans generate a speed signal consisting of a train of pulses (2 per revolution) that is sent back to the mobo header for counting to measure fan speed. The mobo header can count only ONE incoming pulse sequence. If you try to send it two speed signals, they never are exactly the same and so they weave in and out of synchronization, and the counting circuit gets a constantly-changing set of pulses roughly twice as many as it should. The speed result displayed swings wildly and causes confusion. This can be important for the main function of that speed signal - failure detection. The mobo checks the speed signal and, if it gets none for a while, it interprets that to mean the fan is not turning and sends out an error message. On some mobos, specifically for the CPU_FAN header (not for others) it may completely shut down the system as a precaution, not even waiting for the temperature as measured inside the CPU chip to go high.
Second, control strategy. We speak all the time of fan speed control because that is the obvious effect we notice. But in truth, the mobo is executing a TEMPERATURE control action. For the CPU, there is a temperature sensor built into the chip by its maker, and the mobo gets that from a chip pin. It compares that to the target temperature for normal operation of that chip type (custom target depends on the chip type, and the BIOS has to have that info) and changes the fan speed to make the temperature come to target. It will speed up or slow down the fan speed as much as it needs so that the target temperature is achieved. It really does not care what that fan speed is, and does NOT use the fan speed signal as part of its automatic control strategy. In most mobos there are two basic automatic temperature control systems. One works on the CPU internal temperature and that governs the fan plugged into the CPU_FAN header. The other, guided by a different temperature sensor built into the mobo at a spot its designers judge important, controls the case ventilation fans on the SYS_FAN or CHA_FAN headers. Some mobos include extra temperature sensors and allow you to select which sensor is used to guide each SYS_FAN header separately.
Third, METHOD of control. The older 3-pin fan design achieves changes of fan speed by varying the voltage supplied to the fan motor. The connections in that system are: Ground on Pin #1, +VDC supply on Pin #2, and Speed Pulse signal returning to the mobo on Pin #3. The voltage supplied ranges from +12 VDC for full speed down to about +5 VDC minimum. Lower voltage than that may cause a fan motor to stall and not re-start until the mobo system detects that failure and boosts the voltage in an attempt to get it going again.
The new 4-pin fan design does things differently, but keeps several of those electrical signals the same or similar for backwards compatibility features. Its connections are: Ground on Pin #1 (same); +VDC supply on Pin #2 (BUT this time it's a fixed +12 VDC always); Speed Pulse signal return on Pin #3 (same); and PWM signal on Pin #4 (new added). This fan type has a small chip inside the motor case that applies the PWM signal to the +12 VDC supply to alter the current flowing though the motor windings, thus achieving speed changes.
The mechanical arrangement of the connectors of the two systems are VERY similar, so you CAN plug any 3- or 4-pin fans into any 3- or 4-pin fan header. BUT what happens when you mis-match? There are two possibilities. If you plug a 3-pin fan into a 4-pin header, the fan gets a fixed +12 VDC on Pin #2, and never gets the PWM signal from Pin #4 because it could not use it anyway. So this fan will run at full speed all the time. It DOES do good cooling for you, but the mobo has no way to control its speed. Limited compatibility of systems in this case. If instead you plug a 4-pin fan into a 3-pin header, the fan gets no PWM signal to work with so it cannot alter the voltage supplied. BUT that supply on Pin #2 is VARYING from 12 to 5 VDC, and so the un-modified voltage supply DOES power the fan AND control its speed. Although this method of controlling a 4-pin fan is not quite as good as the "proper" PWM Mode, it works and gives almost complete "backwards compatibility" of the new design with the old system.
This also gives rise to a major source of confusion. Because BOTH fan types can be speed-controlled by a 3-pin header that uses the older Voltage Control Mode, many mobos use only that method and trust that users will not notice or care because their fans ARE under automatic control. And just to ensure the users don't worry, they always use only 4 pins on the headers, no matter which method of control the header uses electrically. So the pin count on the header can NOT tell you which method of control it uses, and your attempts to match fan type to header control method are made much more difficult.
Another source of trouble is that many case makers include pre-installed fans, but almost always they include the (slightly) cheaper 3-pin ones. IF you have a mobo that can have its CHA_FAN headers' control method set to the correct one for your fans, you are OK. If not, there are ways to adjust but it's not just plug-and-play.
It gets more complicated when we get to Splitters and Hubs. They are different devices although both are used to connect more than one fan to a single fan header. A SPLITTER has only two types of cable "arms". There is ONE arm ending in a FEMALE (with holes) connector that plugs into the male mobo fan header. Then there are two or more arms each ending in MALE fan connectors to plug your fans into. There are NO other arm types in a Splitter. Because of the almost-identical arrangement of signals, you can use either a 3-pin or a 4-pin Splitter with 3-pin fans, but you really need a 4-pin Splitter with 4-pin fans if the mobo header is using PWM Mode for control. All a Splitter does is connect the Ground and +VDC lines of all the fans to the mobo header pins and they share the power. Only ONE fan's speed signal is sent back to the mobo to avoid trouble with the counting circuit. The big limiting factor here is that most mobo fan headers can supply up to 1.0 amps current max for ALL of its fans in total, so you must not try to connect more electrical load than that using a Splitter.
HUBS are different and sometimes confusing. That's because a HUB can be made to look a lot like a Splitter, with only groups of cables and wires. There are many Hubs that are boxes or circuit boards, too, so they look different but do the same thing. A HUB has the same single connection to a mobo fan header, and two or more (often many) output connectors for fans. Then it has one ADDITIONAL arm type that must connect to a power output from the PSU. Hubs are designed almost always (one or two exceptions) for 4-pin fan systems ONLY. The connection to the PSU provides the VDC power for ALL of its fans, so the Hub is not limited by the current limit of the mobo header. Then the HUB takes the PWM signal from the mobo header and simply shares it to all its fans, and this does NOT overload the header. Finally, it returns to the mobo header the speed signal from ONE of its fans. This system depends on the 4-pin fan design. It REQUIRES that there be a PWM signal available from the mobo header, and it REQUIRES that all the fans accept a fixed +12 VDC supply and each does its own modification of that supply, using the shared PWM signal, to achieve speed control. A HUB thus can NOT control the speed of a 3-pin fan, any more than a 4-pin header can.
OP, when you use either a Hub or a Splitter, you really should have ONLY one type of fan connected to it. That is because all of the fans get exactly the same signal type, and so all of them MUST be able to respond to that control system the same way. There is an exception to this rule when the mobo header involved is using Voltage Control Mode (aka DC Mode). In that case, a SPLITTER can supply those signals to both 3- and 4-pin fans and they all will be under control, because the 4-pin fan has that backwards compatibility feature to use this signal system. However, when using a SPLITTER you are limited to the 1.0 amp capacity of the header.
OP, for your specific situation with two fans each of both types included with your case, the simplest solution MAY be available IF you have two things:
(a) your mobo's CHA_FAN headers all can be configured for either DC Mode or PWM Mode.
(b) You have at least two such headers to use.
If you have those things, then you can buy two 4-pin SPLITTERS. Use one of them to connect both 3-pin fans to a header and configure it to use DC Mode for control. Use the other Splitter to connect the 4-pin fans to a different header and configure it to use PWM Mode for control. If you post back here exactly what mobo model you have we can check the manual for its capabilities. If that simple approach can not be used there are other alternatives we can discuss when we have the mobo and fan model details.