The bot's been leaving talk page messages claiming it has added archive urls, when all it has done is add/modify the deadurl= and df= parameters. I'm not sure such relatively less significant changes need a talk page message (existing archive urls were presumably checked at the time they were added by users), but if you do have such messages, they should at least be accurate. Perhaps something along the lines of "Set dead-url=yes for <url> with pre-existing archive url <archiveurl>".
Has happened under versions 1.5.7 and 1.5.6 (at least):
https://en.wikipedia.org/w/index.php?title=Forrest_Highway&type=revision&diff=805128547&oldid=803727208 - https://en.wikipedia.org/w/index.php?title=Talk:Forrest_Highway&curid=18486189&diff=805128552&oldid=803727213 (v1.5.7);
https://en.wikipedia.org/w/index.php?title=Gateway_WA&curid=44980780&diff=804892830&oldid=801380113 - https://en.wikipedia.org/w/index.php?title=Talk:Gateway_WA&curid=45215227&diff=804892831&oldid=758951420 (v1.5.6);
https://en.wikipedia.org/w/index.php?title=Garratt_Road_Bridge&curid=44747919&diff=804787461&oldid=769423082 - https://en.wikipedia.org/w/index.php?title=Talk:Garratt_Road_Bridge&curid=44798718&diff=804787463&oldid=791544631 (v1.5.6).
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Is this an issue that needs fixing necessarily? It doesn't seem like a too serious of an issue. Internally it destroys and rebuilds the citation from the ground up, so from the bot's perspective it does add an archive, so fixing this is no easy matter.
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It's more of an annoyance rather than a "serious" issue. And potentially a timewaster, since the bot is suggesting a human check an archive that's already been checked by a human.
I've set the priority on this to lowest - I wouldn't want you to spend a lot of time on this if its going to be that difficult, but maybe you could keep this in mind for the future, if you happen to be making major changes to the relevant code when fixing other bugs or adding features.