Yes, there is a conflict/dependency here with multipart form support for the fileEntry and mobi:commandButton. The fileEntry is slated to have multipart support in the next release. What features of the mobi:commandButton did you want to use?
There's no jira for the conflict between ICEmobile and the Ace fileEntry specifically because multipart forms is a known constraint when using the ICEmobile library. There is a jira for the fileEntry multipart support however the jira for multipart support in the Ace fileEntry component is here: