i am sure there will be more reasons coming but I used to get that effect using powdered gloves when handling the reagents and film and it was lessened on changing to powder free gloves. Some smaller marks can also be generated by dust on the rollers of automated film processors as pressure marks develop as dark spots. Filtering your hybridisation solution should also remove particles of dust which can cause this effect.good luck
I agree with Paul Rutland in filtering your hybridization solution, you can also filter your transfer solution. I have never worn powdered gloves so I don't know about that. Prehybridization not long enough or the stringency of you washes not high enough can also do that. Lastly be sure your filter is absolutely dry before putting it to film.