This is going to sound really stupid for a Sci-Fi, but here goes.
When they go beyond a reasonable suspension of disbelief. Problem with that is it's subjective. But for me, it's when they put way too much insane things in it, to a point that I just can't buy it.
The new Doctor Who is a Sci-Fi that does that for me (I'll be dead before I post this). So the doctor is basically an alien Jesus... Oookkaaayyy, fine, whatever. Also he has a time machine that goes everywhere in milliseconds.... so we're denouncing any laws of physics too? Do you have an explanation for that? No? sigh. Also theirs aliens in this galax- ok I'm gunna have to stop you there. If so, where the hell were they, and why haven't we seen them? and don't tell me they're "Hiding the Truth" from us, those aliens go in public places and mass murder people for little rhyme or reason. Also, the one time they do acknowledge it, the press says it's fake, despite the fact that ANYONE near big ben that day SAW WHAT HAPPENED! In face, how do you explain that otherwise? Why would big ben be destroyed? A kid threw a rock at it?
I'm gunna stop there because I could go on for hours. Basically, to me, a good Sci-Fi is one that at least gives a somewhat decent explanation. You need to support the suspension of disbelief, not try to see how much you can get away with until we just say fuck it.
P.S. I'm aware that some of this stuff is somewhat explained, like Big Ben getting destroyed, "They didn't want to believe the truth". That still doesn't explain a lot...