This implied that time also had a beginning and, as a consequence, questions about who or what caused it (necessitating a past tense in time before time was created) were invalid.
Holes in our theories exemplifies the lack of understanding we have. Naturally, people ask questions about these holes, which pushes us closer to a more complete understanding when those holes are filled. Most of the theories that people take for granted have their own problems, and some of those problems have their own theories.
The big bang has the horizon problem (and you may consider dark matter another problem, I do!). There is a theory on this though. I forget the physists name, but his theory says the speed of light has changed over a long period of time, which should get rid of the need for inflation.
The big bang also raises the question "What caused the bang?" M Theory provides an explanation for this. M theory says that their are branes on a higher level than our universe. When those branes collide, a big bang happens. If you are interested, go to nova.org and search for the elegant universe.
The pioneer anomaly shows us another lack of our understanding. I haven't read any theories on this.
Evolution has a long list, that I cant find right now! One problem (I cant remember the name for it) is that evolution cant explain how simple systems came about, because without one part, the system fails.
Sorry to leave topic for a second there, just want to show that many if not most of our theories still need work.