We encountered the same thing today with two nurturing campaigns. Same person received both emails simultaneously despite a 1 email per day communication limit. Logged a support case for this because this will definitely be a possible occurrence in our environment.
It takes nine minutes (give or take) for Marketo to process the fact that someone received an email, so if your programs all send out emails at the same time people can receive multiple emails within a span of 10 minutes. You aren't giving the database enough time to update the status. This is easily fixed by varying your send times.
I always vary my send times by at least 15 minutes across programs.
Marketo support confirmed that it can take up to 15 minutes for a email to be added to the database so the current workaround is to ensure that scheduled casts are 30 minutes apart at a minimum to be safe.
Support also confirmed that there are plans to upgrade this to reduce the lag in logging the emails, but there was no time frame on that improvement.