It seems that after every called timeout another 3-5 seconds run off the clock before the next play.

Is this expected behavior?

The clock runs for a few seconds before the timeout is called, the game center scoreboard doesn't update (something I probably need to fix, I'll put a ticket in for it)

In hurry up situations, I don't think the clock should run more than 1 second after the play is over when a timeout is called.

If that happened in real life, everybody would be talking about how poor the clock management was. You often see players go down and someone is immediately calling timeout.

I have a question about the timeout logic. I have played at least three games when this has happened to me..
http://cust10.myfootballnow.com/watch/179#34175

is this just a glitch that passes on through sometimes, or does my team think adjustments should be made after a 34 yard run? (hopefully they don't, haha)

Any time a team calls a timeout when they're not in a hurry up situation, it is a burned timeout which just means that something went awry and you can just imagine that the head coach is furious that he had to take it.

Is it totally random or linked to the coaching staff ratings?

I need to see a 'Furious' ratings bar in coach build

There are lots of times during NFL games that teams call timeouts on Offense, even on Defense. Could be that they didnt like the D that was lined up against them ot they just had trouble getting the play or subs into game in time.

It's mostly random but is influenced by crowd noise.

Wow that is excellent!