We have been experiencing a number of issues regarding the user shops lately.
We pushed live several updates:
If the item amount = 0 (an illogical) then it is excluded from shop search results
If the item amount = 0 (an illogical) then it is also excluded from Autopricer processing
When you merge a shop, it will automatically restack your items. We posted a quick fix a bit ago where you'd need to manually restack when you merge shops, but we have automated the process now. We also strongly advise users that have merged shops together before to go to Edit Shop and hit "Restack Items" - this will cut down on a lot of noise in user shop/searches
Please let us know if there are any other related issues that we can look into it.