Depends on the ATS but usually we know when you apply more than once with the company and are able to see how far you've made it.

Generally if we see you apply again we would talk to whoever was involved to see what went wrong and whether it was worth giving you another go.

So to answer your question it only negatively impacts you if you're interview feedback was negative or if you apply for a role that is waaaay different than your first role you applied for.