Thank you, all.
We have received an update from Marketo Support that they were able to find the cause of our problem.
Apparently, Marketo forms embedded into pages that we are hosting (outside of Marketo), retained a piece of code that should have been removed. Specifically, point 5.4 of Marketo instructions asks to clear the value for the _mkt_trk input:
Old: <input type="hidden" name="_mkt_trk" value="id:066-WBT-195" />
New: <input type="hidden" name="_mkt_trk" value="" />
Put a Marketo Form on a Non- Marketo Page: http://community.marketo.com/MarketoArticle?id=kA050000000KyqgCAC
As a result of this error here's what was happening.
A legitimate user visited our page, filled out a form, and shortly after, a bot visited the same page and attempted to submit to the same form without filling in any values. Because the _mkt_trk value wasn't removed from the code, the bot was able to associate itself with the last know visit, using tracking parameters/code that were on the page/Marketo form.
That was the missing piece of the puzzle and the one we were stressing on the most. Thanks to Marketo engineers/support for identifying the problem and we are currently in the process of fixing the code on all Marketo forms embedded outside of Marketo.