Input system not working sometimes

It is my first time using the Unity Input System so active and have some issues. First, I had a small issue that input through code does not register, but it easily could be fixed by editing the code and saving (like adding a random debug log). It was okay for me but our game has multiple controls and currently, I also have issues with UI control too(I use a gamepad and keyboard). It works with the mouse but for some reason, I started to get an issue with choosing the button(clicking) with the keyboard and gamepad; And now I can’t even switch between buttons using the keyboard and gamepad. Is it a regular issue with the input system or it can be because we use both new and old systems? Is there a way to fix it permanently or should I just use old system?