This comes up sometimes, unfortunately it doesn't have an easy solution. The state of the drop-down for the tags macro is made assuming that each tag will only be shown once in each tiddler, which for the normal tag field is correct. When you put tags in the tiddler body this isn't enforced and you get errors.
This has come up in the past and someone may have a solution I haven't seen, but unless you give each instance in a tiddler some unique id value I don't think it is possible.