Children cannot be fined or banned for overstaying, but their passport does get stamped with an Overstay stamp. Not likely to be an issue, unless they plan to stay long-term and go to school here.
Although Thailand does not require 6 months validity as long as the passport is valid for the duration of stay, most airlines don't seem to accept this over an abundance of caution. I have been in this situation although over a land border and although the UK Embassy told me I needed 6 months, they were wrong and I was admitted. Your situation is tricky as it may be more difficult to convince the airline check-in. A letter from someone in authority in Thailand may help. Good luck.