Well, you already recognized two of the things that can cause this. You may be tooling while the leather is till too wet, and depending on the tool used you may be striking too hard. The over wet leather is probably the most likely of the two, but the smaller the face of the tool used, the lighter the stroke. Also close knit patterns like basket weave are more prone to cause stretching.
You can mitigate this buy lining your project prior to tooling, or using clear packing tape on the flesh side prior to tooling and then remove after the project is tooled and DRY. Masking tape will also work
It is a combination of all these factors, moisture content, strike force relative to tool choice and permanent or temporary lining.......and experience never hurts which unfortunately cannot be rushed.
Good Luck
Paul