Its worth mentioning that a "Flag" on an app doesn't mean a show stopper. Its just that, a flag, that when they go over you app with you they will ask you to explain it. If it took 5-6 years for you to work full time to pay your own way through engineering school thats a much better reason for that flag than following Phish around (good lord they suck so bad) getting a degree in ceramics with a minor in feelings while leaching off of daddy's money.
There are many "flags". Speeding tickets are a flag, and most people have them. Long periods of unemployment not associated with other acceptable things like education or medical events are another.
Not working holidays is a flag. Did you sick out for them all the time? Or were you just senior enough to hold them off? Big difference.
There's a million reasons for an app to be flagged. Probably most pilots hired had some flags. Its just something they want to look into thats all.