I learnt to shoot handguns in my military service, with a Browning Hi Power in 9mm.
Many years later I taught my GF (now my wife)to shoot, and we started off with her shooting my 0.40. (BAD mistake!!
she ended up liking it so much that for years I had to reload over a thousand rounds a month for her, and she still refers to one of my favourite guns as "Her Browning")
She became confident and proficient fairly quickly and ended up being a regular member in the shooting club where I was shooting regularly at the time. and later qualified as an instructor, working mainly with novices at an indoor range. ( her carry gun is a Glock in 0.357 Sig)
So my answer is no, learning to shoot with a 9mm, 38Spcl, etc does not necessarily need to give you bad habits.
This does not mean that you should start a new shooter with a 44 Mag; a 9mm, 0.40, 38, or 0.45 (or similar), with normal loads ( not +Ps or extra hot stuff) should do just fine.
Brgds,
Danny