Users are assigned both O365 E3 and O365 F3 License. I am trying to see what are the issues that can be caused by this kind of assignment.
You waste money :) And depending on the order the licenses are applied, you might run into "incompatible services" error (forgot the right wording here, sorry). Generally speaking, you should have no reason to assign F3 license to a user already assigned an E3, the latter includes all services of F3.
Please check michev's reply.
Generally, to get better user experience, it's suggested to assign one license.
In this case, you could just assign the Office 365 E3 license to users rather than Office 365 F3 license as the former includes all services of the latter.
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