This question comes up a lot, I really should make it part of my FAQ. :)

It's quite common to get cankor sores while cleansing or while just being sick and NOT cleansing, but at least while cleansing it's a more positive sign. ;)

The balance of mucous membranes can be quite tenuous and can be thrown off by:
the body shedding toxins and otherwise upsetting its pH balance
not enough friendly microbes
toothpastes with sudsing agents - use baking soda
too many citrus/tropical juices, concentrated fruit juices or vitamin C
Not enough EFAs or coconut oil - you can use it topically and it should help.
Sugar Sugar sugar

Once the balance is thrown off, that leaves the skin vulnerable to herpes-like viruses.
Sometimes there is an allergic problem or immune issue going on. Sometimes it's due to deficiency, usually minerals, especially salt, and B vits and A, D.

Hope that helps! :)