In general, I like how Skritter asks you to write both characters of a new word even if you already "know" one of them very well. Since Skritter provides you with pinyin sans tones, you need to pick the correct character in your mind and then know how to write it.
The weird behavior comes when you encounter a new word, say "shi shang", that you haven't encountered before. You (by "you" I, of course, mean "me") aren't sure which "shi" is correct, so you try a few (事,實), and before you know it, 時 pops up with the angry red border!
I think that if it is your first time seeing a compound, any mistake should count as a blue bordered error (along with any bookkeeping that happens in the background), rather than the embarrassing red error. Your error is associated with the new word, not with the old character.
Also, does anyone else ever have Skritter interpret a 4th tone line as neutral instead? Maybe it's just me.