Hey wisty,

In this case, the indication for me was a subtle thicker line on that segment in viewport, that made me inspect closer and "show points". Overlapping lines or segments appear thicker/darker in MoI viewport, but it is subtle. For the Joined surface "degradation" of a solid without the user realizing, from what Michael has shared in posts here, I think he is considering a more direct notification system if something goes wrong or a solid becomes joined surface, but for now, the details window on top right is your friend.

In general, after some time with the program, you will start to have an idea of what the problem is most of the time. There are many informative posts (Michael's answers are nutshell encyclopedias usually) and video tutorials on youtube from several creators that show workflows and problem solving, when things get tricky. :)