The transfer line is relatively thin metal to keep the temperature correct, and so overtightening can physically deform the metal especially if it has gone through many temperature cycles.
The other common issue is reusing ferrules or overtightening ferrules. Again once there have been heating cycles the ferrule material becomes more brittle and prone to cracking, or deforming if it is tightened repeatedly.
If you are using the brass transfer line nut I strongly encourage you to invest in a "self tightening" column nut instead. They can be tightened by hand, rather than with a wrench, which basically eliminates the possibility of overtightening. For the most leak tight system possible, replace the ferrule if you remove the column from the transfer line and intend to reinstall it. You can probably get away with retightening it a few times.. but is it really worth the risk/down time?
https://www.agilent.com/en/product/gas- ... uts-for-gchere's an example of those nuts--you can get them for either the inlet, the MS, or any GC detectors. The newest model has a removable piece that has a septa like material in it which can be used to hold the position of the column nut when it is removed from inlet or detector. Once it is installed back into the inlet/detector you loosen it and remove it (sadly you cant keep it installed bc the oven will damage the septa-like material. Would be awesome if you could keep it on all the time.)
I ABSOLUTELY HATE those brass nuts.. they cause so many problems.