I just viewed my log.I had a RG and MLB catch passes in the game.Is this something that happens all the time?I did not expect too see these 2 catching passing in a game.

Yep you need a 60 man roster and have available backups or the CPU fills in. You can also go to your misc settings and change the slider for sub in/out. Around 60-70 is about right I'd say

Also, once your starters are pulled you have fewer players available - the #1 and #2 WRs get pulled at that point. You can extend the time your starters play to prevent that a little more, but the best solution is to have all 60 players active.

I will be releasing a patch that will not rest starters if your depth chart for that position is not deep enough, but don't have an ETA on that.

Excellent!