Reasons for oral ulcer, either they are aphtous or not, are multiple. When it can be related to CD, UC, IBS, it may also be unrelated to it.
Vitamines and minerals deficiency may be the cause of them for instance people with B12, folic acid or iron deficiencies are more likely to have ulcers. A person that recently stopped smoking can be more prone to them as well. Some oral allergies may translate in ulcers, either it is from a food trigger or a reaction to chemicals in toothpaste for instance. Herpes can also manifest as mouth ulcers and are likely to be showing with stress, hormonal change or being sick.
There is also a disease, Behcet disease, that can cause ulcers both mouth and genital, along with skins pathologies (boils like), joint issues and eyes inflammation. When it affects the digestive system, it looks a lot like UC or CD. The symptoms list is rather long and they are not always present together.
It worth bringing it to your GI if they occur frequently and maybe it would be worthy to have a referal for a rheumatologist if it is needed.