I've recently learned 朋 ; it is one example of kanji for which renshuu does not have grade-level marks (i.e. 小中高x) on the readings. This seems to cause some undesired behavior:
My "kanji readings to include in quizzes" setting is set to "renshuu recommended"; for such kanji, renshuu seems to be recommending all readings. 朋 isn't particularly bad with respect to this, but some kanji have readings for which renshuu knows no vocabulary (e.g. くろ.い on 黎), and I'd like to avoid being quizzed on those (for now).
If, during the pre-quiz new term introductions, I proactively go into the dictionary and check then uncheck the "Include this reading in my quizzes" checkbox on some readings, the page refreshes straight into the quiz skipping past any remaining introductions. Furthermore, the quiz may include the specific reading that I just excluded, and answering the question will override the exclusion.
I understand how it is working against your expectation, but that is how it is coded (as in, this is not buggy activity). For any of the ones that actually filter based on reading data (school levels, renshuu recc, etc.) I believe it will simply include all of them if you are studying a kanji that does not have any of those markings. At the moment, I have no plans to change this behavior.
As to the second issue, I'd love to see a video of it (you can email it to michael@renshuu.org) so I can prevent that from happening.