Stress in acclimation can be a cause if there is a serious difference between your tank and the LFS. But, IMO, stress to the fish prior to your purchase is more likely the problem. Many stores make fish immediately avail;able for sale when they come in, which means that the fish could have been injured, or exposed to high levels of ammonia, large temperature swings--any one of a variety of stressors--and then into your tank, where it's just been pushed too far to survive. Unfortunately, many species of fish will look healthy and alert from stress--but it just pushes them too far to fully recover.
Depends on the aggression. Some fish just will not ever get along with others, and putting them in a species only tank, or removing the other fish, are the best options. I removed everything but the bottom dwellers from my 55 when I had my black paradise--he was brutal, and intolerant of anything that spent time in the upper water column. He completely ignored the cories, plecos, whiptails, and loach. Some fish just have to establish a ehirarchy, and letting them argue it out, as long as no wounds or injuries occur, is fine. Some fish just have a high level of activity--like danios--and while they aren't aggressive, they certainly stress peaceful fish. I don't have danios for this very reason--they don't fit in my tanks.