Mine is caused by both-at the moment the gum inflammation is mimicing my gut inflammation. I can tell when my TI is getting irritated/more inflamed by 2 things(other than pain and weight loss):
1) My JRA gets worse
2) Gum inflammation
The reason CD patients get the mouth ulcers is usually because their intestines are inflamed, hence the inflammation in the mouth. The inflammation from your gut circulates through your blood and that inflammation can attack anything. For me, It's my joints and Gums. For others, it's the eyes and skin. More than half of your immune system is in your gut. When the intestines are inflamed, your immune system is lowered. Add to that bacteria, antibiotics, immunosupressants, poor absorption of minerals/vitamins and you can BET that your immune system is lowered. When your immune system is lowered, it can't prevent that inflammation in the blood from circulating. This is why people with Rhuematoid arthritis RARELY get infections on Remicade. Their joints are the first thing being attacked and since your immune system isn't in your joints, you probably won't have much of an issue with an increased infection risk.
You can get bloodwork done to check for the nutritional deficiencies. I haven't had NEARLY as many mouth sores/inflammation since I've been put on Folic Acid & Vitamin B12. When my gut is inflamed and I'm not absorbing as much nutrients, the mouth sores get worse/come back.
A biopsy can determine if you have any granulomas which will confirm CD but the chance of the granulomas showing up is 50/50. It can take years for them to show up and when biopsied, it needs to be done in the inflamed area. Once you get CD, usually your CD STAYS in the same place where you had inflammation in your first flare. It doesn't spread(unless you have a resection). You may say "Well my Crohn's didn't show granulomas in my colon with my first flare and now, 5 years later, there are granulomas." The logic there is wrong. It's more than possible the GI didn't biopsy the right part of the intestine to show CD in the colon when you were first diagnosed with your first flare. There is a insanely high chance you've had colon inflammation the whole time but the inflammation was worse in another area so that's where your GI focused on the treatment of the disease rather than the mildly inflamed colon.
I know that's a lot of information but in conclusion: If your GI hasn't already diagnosed oral Crohn's and you didn't have any mouth inflammation with your very first flare, but you are now having inflammation in your mouth with another flare, you don't have oral Crohn's. Your body is just reacting to the inflammation in the gut and the gum inflammation is your body's way of saying "HEY! I'M INFLAMED IN THE GUT! FIX ME!" Just like how menstural cramps is the body's way of saying "I'm about to lay a egg"