Thank you for your reponses!
The reason we didn't set up geotargetting within GWT was that our site is both multi-regional and multilingual. Our site is similar to Google's example below.
"it would make sense to set a target of Canada for a site about restaurants in Montreal; but it would not make sense to set the same target for a site that targets French speakers in France, Canada, and Mali." - Google
We have Spanish sites in Mexico and Spain targeting Spanish speakers. The "es" and "en" were set as a default to target users in countries we do not cover.
After implementing the rel alternate hreflang tags, we were hoping to resolve this problem but it didn't clean up Google's SERPs.
Any suggestions?