I've changed all patch file from .ctr to .big (as requested in the Readme file).
That is the problem. Installing the mod manually will cause the vanilla game and other mods not to work. You are supposed to use the Contra Launcher, which enables the mod's files when you launch the game, and disables them when you exit.
Manual installation is required only if you cannot run the launcher for whatever reason. You have to rename all files back to disable the mod.
If you installed Contra manually on purpose and don't want to do this process every time, make a copy of your game folder (without ShockWave and Rise of the Reds) and install Contra there.