but I tried out my idea an its working really well
I just put resistors between the emitters and the wire going to the arduino plus.
I'm still not really sure where capacitors are needed.
How do I deal with this? Would replacing the power transistors with mosfets help?
You ommited the value of the most important resistors in the circuit! The resistors for each LED segment.
Resistor values posted on attached image, the resistors from the LEDs are 1 watt 4.3, 4.3 & 6.6 ohms for the different colors (blue, green, and red, respectively)
But your circuit is explicitly designed so that EACH regulator supplies power to THREE LEDs. I don't understand this issue?
Do they get warm?
How much voltage drop? How much current? Those 2N5191 are pretty low gain. It appears that you aren't fully turning them on ("saturating" them) and that is causing your voltage drop and overheating. You may have to make a DIY "Darlington Pair" and use another small transistor to fully turn on the 2N5191s.
If it were me, I would abandon all those voltage regulators and just get a more suitable LED power supply. You can probably get a nice 5V or even 3.3V supply from a surplus place (or charity shop) for practically nothing. Keep it simple. Your scheme with all those regulators is WAY too complex and problematic IMHO.