List of problems TFF faced:
1) No ILM, not even the C team. This was the first time Trek had to go outside the ILM framework to get their effects done and unfortunately, it showed.
2) Writers' Strike. Shatner was unable to get the script professionally treated and submitted to a lengthy editing process by the guy he wanted. It ended up being rushed and that showed, too.
3) Teamsters' Strike. Many location shots had to either be altered or canceled because they simply could not get the cameras and crew out. Teamsters are not people you want to mess with. Many of the location vehicles experienced 'unexplained' breakdowns. They were harassed and threatened.
4) Paramount. They saw TVH's big profit and its humorous tone and demanded constant efforts to 'lighten' it up. Written by an experienced writer, this would not have been a problem. Unfortunately, the guy was inexperienced, leading to bumping heads, getting lost and all sorts of other business.
5) TNG. This was the first movie to be done concurrently with a Trek TV production. Paramount decided this would be a good way to lower costs as much as they could, reusing TNG sets and 'reasoning' that the movie shouldn't get more since they already were paying for TV Trek.