Only 20 imperfect negatives so far? I've been doing it for many years, and I've screwed up a lot more than that!
Seriously, it takes practice. Be patient - you will develop a process that works for you - eventually.
Are the edges of the spots hard or soft?
If they are hard edges, they may be air bubbles.
Two per tray, and agitation every 60 seconds? How long does the agitation last?
I process sheet film in a slosher, six sheets at a time, with 5s of agitation every 30 sec. 30 sec of continuous agitation up front. Also - and this is controversial - I use a presoak. No scratches, even development.