coming and come in?

I was in upstair, my friend knocked the door, and said " come in", but he thought I said " coming", so he waited for me, is there any way to avoid this mistake?

Yes. Stress the word "in" rather than "come".

Stress 'in' so he knows it's 'come in' not 'commin'. Or you could also say 'come on in'.

Yeah, "come on in" is used a lot in American sitcoms.