Below a list of know bugs, issues, & other quirks* of BizTalk 2013 R2 (mainly CU3) and Visual Studio 2013 (update 4) , but I will update with fixes as the CUs come out or when I know about a new issue, so if you have another one I will add it (and link to it if you have a blog about it) if you let me know. This in addition to the ones listed by Microsoft on Known Issues in Installation, Configuration, and Deployment
* My definitions for classifying these are
Bug: Causes negative impact and no known work around or requires a lot of effort to work around.
Issue: Causes negative impact but has an easy or quick work around.
Missing: A feature that BizTalk doesn’t have that would make our life easier.
Quirk: Something strange or unusual but does not cause a negative impact so far as known.