What exactly did Barry do in "Rogue Time" to change things so badly?

The Flash S1E16, "Rogue Time", starts out right where the previous episode left off, with Barry having just traveled back in time 24 hours. Wells almost immediately picks up on it and warns him not to change things, but of course, he does. This has the expected terrible unintended consequences.

However, the things that happen as a result of Barry's meddling don't make any sense. The only major change Barry made was his premature handling of the previous episodes meta-human villain. The changes to the timeline that result don't seem to have anything to do with the villain Barry nabbed:

and:

Even when Wells is warning Barry of how badly he messed up, he remains very vague; basically saying that "time" was going to try to get even for Barry messing with it.

Are they trying to imply that that time/karma/destiny is somehow actively screwing with Barry's life to get back at him for "cheating"? Or is there some subtle connection between all of these events that I missed?