How to troubleshoot Scheduled Reminders
Thanks to @jaapjansma from CiviCoop for all his help and support. The issue has now been solved and merged into the main CiviRules development, if anyone is facing this issue, check out the fix and PR here.

As an answer (kind of) to the question:

I couldn't find a straightforward way to debug so, in this case the Reminder Sent or Membership Reminder sent  activity that Civi creates when a Schedule reminder is triggered wasn't created, that was the lead to investigate, using CiviCRM's debugging documentation (in a test environment, of course), turned out that the activity was created but with improper values, therefore the Schedule Reminder cron job would keep sending messages until the activity was completed.

Posting this as an answer just for the record.