What kind of film is this? Traditional grain film just starts to clear in rapid fixer in about 30 seconds and takes at least 2 minutes to completely clear. If you are using T-grain film like Tmax, then double or triple that.... Ilford makes at least two different fixers... which one are you using?
When you look at your film, does it look milky? If so, it's way under fixed.
Dots can be anything.... but I think the first order of business is to make sure your steps and processes are right.
If you tell us what film you are using and chemistry (and how long in each), some of us can help you.