I'm getting allot of this in preseason games. My QB just got a interception, my punter is returning kicks, my guard is running the ball...

Same here,but this was my first game so maybe it`s a rookie mistake.

How many players can be active in the pre-season because I only have 46.If it`s 60, that may be where the problem lies.

You can (and should) activate all 60 players during the pre-season. What is happening is because the players are not in full conditioning, they are being subbed out more than they will during the regular season. If you run out of players, the AI will just put in the best player available based on their bars, and when no one really has the bars you get some strange results. Also, once you reach the point in your Misc game plan settings to pull your starters, the #1 in most positions will be benched, so if you don't have enough depth to finish the game you'll get more strange substitutions. If you just plain don't have enough players because of salary cap issues, you may want to keep your starters in longer (but because they're not fully conditioned you are also risking more injury).

The other big issue is under Misc in the game planning screen at the bottom. If you pull your starters after the 1st, 2nd, or 3rd quarters in the preseason, then the backups are the starters in those quarters. When they get tired, your starter is out for the game because you benched them, so someone else on the depth chart will fill in for backups. I had WRs and linemen running the ball as my RB in the 3rd and 4th quarters because I benched my starters after the 1st half.

That is usually the biggest issue causing out of position players in the preseason. So check your settings for pulling starters and just set it to 'never' and start your backups if you want them to get the experience and conditioning.

I understand all of that. Still a 200lb punter should never be put in as a defensive tackle.