Running data integrity it would appear that these questions are the culprit:
The following questions should be deleted:
QID `687` because `No matching group (47)`
QID `688` because `No matching group (47)`
QID `689` because `No matching group (47)`
QID `690` because `No matching group (47)`
QID `691` because `No matching group (47)`
QID `692` because `No matching group (47)`
QID `694` because `No matching group (47)`
QID `695` because `No matching group (47)`
QID `696` because `No matching group (47)`
QID `697` because `No matching group (47)`
QID `698` because `No matching group (47)`
QID `702` because `No matching group (48)`
QID `703` because `No matching group (48)`
QID `704` because `No matching group (48)`
These are all good sub-questions that I did not delete. I did however move the main question for each of those sub-questions to a different group. It would appear the sub-question GID wasn't updated properly and left these sub-questions hanging.
Running these two queries has fixed the problem. I am assuming this is a bug in lime survey?
update lime_questions set gid=46 where gid=48;
update lime_questions set gid=46 where gid=47;