Some complaints I have seen thus far:
Why would Claire think she could kill Peter?
Status: Resolved.
How is Linderman back from the dead when he had a hole in his head?
Status: Resolved.
Why didn't Peter use his powers in the bank?
Status: Resolved.
We are not even a full month into the season, folks. Speculation is fun, but really, the expectation that they lay all their cards out on the table that seems to follow this show is bordering on the realm of ludicrous. Yes, there have been some flubs that really should be resolved already (Peter's omnipresent future scar, what's up with Sylar's powers*, where is Caitlin**), but they tend to get around to shit eventually and this season in particular seems to be moving at a very swift pace in terms of answers. Again, we're less than a month in and we've already seen so many questions raised and then answered rather swiftly while weaving in new ones. This is how serialized fiction works.
*This has actually been answered by the writers. When he contracted the Shanti virus, he lost every ability except his telekinesis. His nuclear and future panting abilities are, according to them, the result of Sylar taking the abilities from others again (As we are well aware that powers do repeat and he is clearly not over his tendencies by a long shot as yet). I don't necessarily count this as a full on resolution since it was answered in interviews rather than in the actual show.
**This was set to be resolved, but has since been completely fucked by the writers' strike. It was supposed to be taken care of in the latter half of season 2, but when the strike occurred, the situation became a difficult one. Aside from the fact they had to completely and drastically rewrite the ending to volume 2 (And I mean DRASTICALLY, some of the shit I've heard whispered was pretty severe), scheduling conflicts with minor characters likely came up. That's also why Candice was killed off. She was originally supposed to pal around with Sylar for a while, but Missy Peregrim left the show and by the time they realized they really dug the temporary replacement actress, an entire restructuring of the season would have been necessary to write her back in.
In summation: Watch the show, people. Your questions will 90% likely be answered in due time, provided we don't see another strike.
Edit: For those curious, I get most of the behind the scenes info I reference here from Comic Book Resources' weekly article
Behind the Eclipse, which they run every Monday afternoon covering questions submitted concerning the prior week's episode.