Unexplained Crashing

It's barely been a couple of month since I've used Unity 4.5 for the purpose of contract work and I've experienced more than a few odd issues. Among them, the most prominent are:

• Missing references to sprites in the scene
• Even after pulling a fresh build from the repository, the issue persists. Weirder still, my team-mates were supposedly free from this issue when they opened the scene on their end.
• Scene simply crashes when I attempt to open it. Making an executable is impossible so long as the said scene is included under "Build Settings"
• A team member pointed me to http://docs.unity3d.com/Manual/LogFiles.html to check out the local crash log. Unfortunately, I still could not identify the source of the crash.

As a last resort, I deleted the entire "Library" folder (possibly a dangerous move). That somehow fixed the above 2 issues.

I wish someone could shed some light on these issues.