The Phineas and Ferb Effect (the phenomenon not the episode) answers several questions from Phineas and Ferb, the biggest one being the "Mysterious Force" Candace talks about in the movie "Across the Second Dimension". She refers to it as something that always thwarts her efforts to bust the boys. Now being caught and punished by their mother, if At Last and Quantum Boogalo are an indicator, is definitely things going wrong for the boys. Now consider that the Phineas and Ferb effect is effectively an Anti-Murphy's Law, where everything is slanted towards things going 'right' for the boys. And consider the insane domino effect seen from Murphy's law sometimes. Clearly it's the P&F Effect that has been thwarting Candace.
Other things it explains are things such as no-one protesting further than "Aren't you a little Young to ... X" "Yes, Yes I am." "Okay then.", the things they order arriving in minutes and the boys finishing projects that, if not impossible, would take years to do, within hours, or the boys and their friends surviving things like the roller coaster being sent into space, and re-entering the atmosphere. The clues were there from day one, we just didn't put them together.
It's been brought up that the reveal of the Phineas and Ferb Effect clashes with continuity, particularly in regards to episodes such as Summer Belongs to You, in which things do go wrong for the gang, however there are three things to consider; number one; events ultimately did work out, despite the gang being stranded on an island they managed to get home, two; due to things going wrong the boys had an adventure, which is ultimately what they want every day, and three; in facing adversity for things going wrong, the boys end up learning valuable lessons that will help them in the future. Furthermore we see through out Phineas and Ferb that the Phineas and Ferb Effect can work in esoteric ways to achieve desirable means (namely the means through which events transpire to make sure Linda doesn't see the boy's inventions), so it's entirely possible that it is indeed the Phineas and Ferb effect making things go wrong in the short time, in order to have things go right later down the line.
