Ego isn't omniscient...he has limitations.
Mantis says that it will take Ego time to realise there are; then when he does find them he's put to sleep for a while and then there's a whole "space battle" going on inside the planet causing immense damage.
He's also trying to control Peter at the same time while the other Guardians are also running around
So, he's distracted and has no reason to know that there is a tiny plant running around inside him and even if he could he has no reason to suspect that it that could cause him damage.
However, we do see Groot being crushed inside the tiny tunnels...so it's possible that Ego does know he's there...but again, what damage could a tiny plant do?