You have two problems.
The one you noticed is the presence of water points on the negatives when the film was put to dry.
Re-washing and drying can help. This may not solve the problem if the emulsion side of the film is affected.
After the fixer bath, wash longer than you have been to remove ALL the fixative absorbed by the emulsion. Always try to keep all liquids at the same temperature to avoid soliciting the emulsion that has absorbed the processing solutions. The swollen emulsion is fragile.
Instead of ordinary water, a 30-second acidic stop bath accomplishes three things: Changing the pH from base to acid will break the developer almost immediately to ensure proper development times. This will help to prevent the fixer from being diluted by the high residual pH introduced into the fix by the developer. AND the change in pH will help compress the swollen emulsion and "extract" more developer from the emulsion faster than ordinary water.
A longer wash allows all the fixative to migrate from within the emulsion to the wash water. That takes time. 20 to 30 minutes is minimal. The archive wash lasts more than one hour unless you use Hypo (fixer) Eliminator. Make sure that the temperature of the wash water is the same as that of your other solutions (optimal between 20 ° C and 68 ° F) and that it does not fluctuate. A quick dive into a diluted wetting agent (according to the instructions – more is not preferable) will reduce the chances of drops forming on the surface of the film. Wash for a minute or two to remove the wetting agent and allow the film to dry in a clean, dust-free place.
(By the way, the water point on the first image is very similar to the ones you find on the negatives whose washing was not enough.The tiny white spots of the larger ones are a symptom that I'm Have already seen with short washes.)
Do not forget that chemicals act in the emulsion and not just on the surface of it.
Your second problem is scratches on the film emulsion caused by scraping the film to remove the water.
Either let the film hang freely to let the water run, or make sure your fingers, your chamois or your blade are perfectly clean, perfectly moist and slightly applied, otherwise the damage will be permanent and difficult to eliminate. (The eye can spot an unwanted scratch line faster than any other pattern I can think of now.)
One more thing ™ The total time in the fixator should be "twice as long as the film takes to clean up." This "time" can be determined experimentally by immersing an untreated film film into the fixer and carefully setting the time required to become transparent. The double of this hour is the correct duration for the fixer bath. Longer than this time is not necessary or useful.