1994 Mercury Cougar door remotes

You can try reprogramming them, if that doesnt work it may be an issue with the controller for the keyless entry system. Here is the procedure for reprogramming

FORD KEY PADS/REMOTES-
1-enter permanent factory code
2-press the 1/2 button within 5 seconds to enter programming mode
3-within 5 seconds enter new code, doors will lock, unlock to verify code, this erases previous codes
remotes will also need to be programmed.
1-insert key, turn ignition off-to- on eight times in succession, ending with key in on position doors will lock, unlock to verify in programming mode
2- Press any button on new remote, doors will lock, unlock to verify
3-Do the previous step with the second remote, doors will lock unlock to verify.
4- turn ignition off. Doors will again lock, unlock to verify