Bad calls? Yes. Conspiracy? No.

49ers hit on Seahawks TE: probably a good call. I can see both sides to the argument. Mike Pereira liked it so I will defer to his judgement.

49ers touchdown reversed: good call, the ball never appeared to break the plane. The injury on the next play is unfortunate, nothing more.

Holding on Aldon Smith by Russell Okung: bad no-call. Pretty clear holding.

Shove OOB by 49ers player: probably bad call. Not enough to draw a 15 yard personal foul.

Hold on Michael Crabtree: can't see it, the video does not give a good angle. I do remember thinking during the game that the Seahawks secondary was given a lot of leeway with regards to downfield contact on receivers that I did not think was consistent with all the other NFL games I watched this season. That trend continued in the Super Bowl, where there were several plays I thought were PI that were no-called.

Block on the back on kick return: not a block in the back.

Intentional grounding not called: from the end zone camera angle it was a close play. I thought Wilson was still in the pocket, but it could go either way.

Running into the punter: one of the two major (possession) calls that the crew got wrong. Clearly roughing the punter.

Marshawn Lynch spot: the video only shows the yellow line, which can be very inaccurate. Still, looks like a generous spot to me.

Aldon Smith offside: I can't hear a whistle. The D line players all know that offside is a play-on situation and they should keep going. They do stop for a second however, which might suggest they heard a whistle.

Navarro Bowman interception/fumble recovery: the second major call missed by the officials. Bowman ripped the ball away from the receiver and was clearly down by contact. The officials held their whistles, which allow Seattle time to pounce on the injured Bowman and simultaneously possess the ball (remember all ties go to the offense).

I do not know anything about the timing issues, someone else will have to address those.