Subject to the rules about including JQ flights, I wouldn't rely on that error message having anything whatsoever to do with the adding JQ.

In my experience, that error message can be displayed for any number of reasons entirely unrelated to what it actually says. It will show, for example, if you have flights that don't meet minimum connection time or of if you've inadvertently gone over the maximum number of allowed segments (both overall and within each region) because the tool has chosen two flights (i.e. indirect) when you want one non-stop. This might be because there's no availability on the non-stop in the right fare bucket or the flight doesn't operate that day.

In all, look at each individual flight segment to see if there's a reason why the entire itinerary isn't working. Don't just look at the JQ flight(s).