Let's call these garage doors number one and number two. I think what you did was program one of the remotes from number one to number two or vice versa. This will cause that problem. What causes confusion is you are not programming the remote, you are teaching the receiver to accept the code from the remote.

Now then what we need to do is go to each motor unit and hold the learn/smart button in for six seconds. This will erase the memory of both units and none of your remotes should work. Take the remote(s) you want to work with number one and press the button on the remote while you press and immediately release the learn/smart button on the motor unit. Do this for each remote you want to operate number one. Now do the same thing for number two. You should be okay.