I'm not a teacher...
To say that a person doesn't currently understand you - you might say:
"I don't think you are understanding me correctly."
However - understand is a present-tense verb. So - the second sentence would be correct, too - meaning that the person doesn't currently/presently understand.
The first sentence would be useful if you were discussing a conversion that was in the past - as in this exchange:
Him: "I missed seeing you yesterday."
You: "I don't thing you understood me correctly, I meant we should meet at the bar."
Student or Learner