Spanish did massacres and killings like any other country did when invading another. And most of the conquistadores army was actually made of native americans that sided with spain.

We did some questionable things, specially against the Incas, but we did it with the help of the natives that didnt like their Inca or Aztec overlords, so, no, there was no genocide as the modern day latin americans are descendants of the natives or a mix between european and natives.

The king even prohibited the enslavement of the natives declaring that they were subjects of the crown, like any other spanish. The only problem were the conquistadores that basically did whatever the hell they wanted, some were even criminals and were imprisoned at some point.