I'm using the tags plugin with tagbase="tags".
Already existing tags, corresponding to pages like tags/foo.html work just fine.
If I add to a page a tag which is not existing (e.g. with ) the just modified page will have a link which point to tags/newtag. This is in theory correct, but in practice leads to creating a tags/newtag subpage of the page I'm editing, while my tagbase is supposed to be relative to the wiki root.
When used in a wiki which already have some tags this leads to mixing up tags located in tags/ and tags located in whatever/tags/.
When a new page is being edited, ikiwiki lets you chose where the page will be created, so you'll get a dropdown list of possible locations for the tag page. You should be able to choose between either tags/foo or page/tags/foo.
The way that ikiwiki decides which location to default to in this box is fairly involved; but in general it will default to creating the page at the same level as the tagged page. So if the tag is on any toplevel page in the wiki, it will default to creating
tags/foo; if the tag is on a page in a subdirectory, it will default to creating subdir/tags/foo.
I personally like this behavior; it allows me to create a subdirectory for a particular thing and use tags that are specific to that thing, which are kept confined to that subdirectory by default. For example, this is used for ikiwiki's own plugins tags, which are all located under plugins/type/* and which apply to pages under plugins/*.
It's clearly not the right default for every situation though. Explcitly setting a tagbase probably lessons the likelyhood that it's the right default for things under that tag base. I'd not be opposed to adding a special case to change the default in this case, or adding a configuration option to change the default globally. On the other hand, it is pretty simple to just check the location and select the right one from the list when creating a new page..