Solution - Learn to read the trainer info. This is must. If you don't, don't complain when a noted incident that's explained in the info occurs.

Solution - Don't use the trainer. Play the game straight so you don't have to deal with the issues that a trainer might cause.

In simple terms any trainer changes the very nature of the game. This change usually significantly favors the player, however sometimes it can cause secondary negative issues. In particular trainers sometimes affect custom scripted sequences.

There's no generic way to resolve these problems, and expecting the trainer coder to modify these one off sections of game code to make it all work seamlessly is silly. It's a massive amount of work.