After a long secondary you'll have much less yeast in suspension, so it's going to take quite a bit longer to bottle condition. Like uberculture says, extra time will not result in bottle bombs. Unless you bottled too soon before fermentation is over, then all bets are off.
Did you take any gravity measurements? In cases like this, a refractometer is really the ideal tool. You can get a measurement from just a drop of liquid, and although the reading will not be 100% accurate you can tell if gravity has stabilized.
What you're seeing when you rack or otherwise disturb the fermenter is dissolved CO2 coming out of solution. It can certainly look like fermentation is starting again, but it's pretty common for the airlock to bubble for a day or two from residual CO2 off-gassing.