When you click on the tag, are you only doing so from the full tags list? Or are you sometimes clicking on the tags from the side bar on the right? If the latter, are you clicking on the "Related Tags" list? If so, please note that the "Related Tags" list is a refinement: it displays the intersection of the current list of tags with the newly clicked one. So if you have, say, [ag.algebraic-geometry] currently and then click on [ap.analysis-pdes], you will end up with a small collection that is tagged both.
(This is just a completely random guess; if it doesn't apply, then you may have found a bug. But I cannot reproduce it on Firefox.)
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