When a service or domain is invoiced for renewal, the services.renew_date is bumped forward (+ term/period, e.g. 1 year, or 1 month, etc), which prevents it from being invoiced again because Blesta is only looking for services set to renew within a set period of time. I'm curious whether the renew_date was being bumped forward on this service/domain or not. Did all the invoices show the same period/date range on the line items? My guess is that something was preventing the renew date from being bumped forward, there may be some errors in your ../logs_blesta/ logs that could give a clue.
Overlapping cron jobs are normally not a problem because Blesta locks the task when it starts it by logging the attempt, then when it's finished it logs the end datetime. Until the end datetime is set, it should not run again. However, it is possible that if multiple cron jobs start at exactly the same time, this may not be detected. In that case you will find in the log_cron table multiple runs that start at the same time and overlap. You should confirm that you have only a single cron job set up for Blesta.
The TLD sync task should not interfere with other tasks and we have no other reports of this. This is because each individual task is locked while it is running and cannot run again until the previous run finishes. If the TLD sync task is taking a long time, then you could have another Blesta cron task run, but it should only process tasks that are not currently running and should be started again.
Can you provide more information?