Congrats on making it so long in life before your first filling!
But actually, it's pretty common to have a small looking bit of decay become more extensive. I'm assuming (from what it sounds like) that the filling was on the biting surface of the tooth. On that part of the tooth, there are grooves that are deep and when decay gets down in there, it looks small but can expand and become very deep. I think I see it about
once a week, where I go to do a filling and it ends up being WAY bigger then I anticipated. Caries on the biting surface is only sometimes visible on a radiograph. Usually, you can't see it.
As Crohn's Disease, there are some oral things that appear. The apthous ulcers (canker sores) are a huge concern to Crohnies. Another concern is constant reflux or vomiting, causes the teeth to be bathed in acid which causes them to almost disintegrate and become more susceptible to decay. I think the biggest concern is really side effect from meds for causing dental decay. Like Entocort causes dry mouth, which causes decay if the teeth aren't bathed in saliva. Prednisone can cause calcium to be leeched from the teeth via the saliva which causes decay. Some of the 5-ASAs can cause dry mouth which is way less common then with Entocort. I'm not sure what/if the oral side effects of the biologics are....
I've only seen two patients with Crohn's in practice so far (and me, so 3) and generally, our teeth aren't the best.... I think it's part side effects from meds and also diet. The softer the diet, the more likely it is to get stuck to the teeth and the more likely it is to induce decay. Additionally, our diets are high in fermentable carbohydrates which promote bacterial growth and decay. I know personally, I have insanely good oral hygeine (brush 3x day, floss 2x day, fluoride rinse and chew sugar free gum) and I still will get cavities from my high sugar/high carb diet. It's sad that as a dentist every one of my back teeth and one of my front teeth has a huge filling on it (some from being a bratty kid and some from Crohn's).
But anyway, the short answer to your question - really common to have big cavities that look little. And the cavities could be CD related as well as not having been to the dentist. Odds are the cavity was there at some point in time, but a sooner dental exam just would have caught it before it got bigger. Probably would not have prevented it (the ones on the grooves of the teeth are almost impossible to prevent without sealants while the ones in between the teeth can be prevented by flossing.)
the long answer, hope it helps.