Can a baby's tooth come in with a cavity already there?

Very Unlikely. Decay comes from exposure and missing areas while brushing along with damaging dietary habits. It is possible however for the tooth to have a deformity that has caused a cavity like lesion that may or may not need to be restored. It is always best to ask your dentist. It is recommended that children be seen first before age 2.
Likely different pbm. Kids with teeth that emerge with color irregularities, wavy lines, etc. Often reflect an interruption of the tooth formation by some illness suffered by mom (&baby) during pregnancy or baby after birth.