Collected comments to avoid the possibility of deletion and if anyone can remember the TV show feel free to edit it in.
When a' wert lad it was a common phrase to use to ask someone if something was wrong (not just in Yorkshire).
I'm not sure but I think the phrase was 'overpopularised' by a 60/70's UK TV serialised drama (which I can't remember the name of) where a young boy would run in to his house and proclaim Mam, Da, come quick, there's trouble at pit.
The pit does indeed mean a shaft coal mine and the trouble was either an accident or a union/worker/boss based problem. It's use now is idiomatic to mean 'a problem'.
Trouble at mill was an even earlier version of the same thing, this time relating to the cotton mills of 19th Century (Northern) England.
There is no shortage of Americans on this site, so perhaps one or two might chime in with their feelings. It is along similar lines to the Lassie phrase Trouble at the old mill. I'm not sure if it's still in use in the UK amongst the younger generation, but I'm confident trouble at mill will still be widely known as it's the older of the two, trouble at pit might have slipped a bit due to the demise of the coal mining industry.
The only TV series I can think of is the 60's drama Inheritance but that was about cotton mills. I keep thinking of Norman Wisdom but that would not have been a series.
Further investigation shows that Inheritance http://en.wikipedia.org/wiki/Inheritance_(TV_series) is the TV show that made trouble at mill a 'catchphrase' which could be what prompted Monty Python to parody it a few years later.
I'm now thinking that possibly When the boat comes in http://en.wikipedia.org/wiki/When_the_Boat_Comes_In popularised trouble at pit.