WRers have discussed at great length the harm that three admin tools -- (un)deletion, (un)protection, and (un)blocking -- can cause. There hasn't been much discussion, though, on formerly-admin tools (rollback and ip block exemption) admin abilities (deleted page viewing, history merges, moves over other articles, rollback granting, unwatched pages, account creation, ip block exemption grant), or the dozens of non-admin tools that can be added to the toolbox (watchlist and live feeds, related changes, citation fixers, history and traffic stats, the spellchecker, etc) or come automatically (undo).
A thorough discussion of Wikipedia's problems should include discussion of the misuse of tools outside of deletion, protection, and blocking.
History merges can be performed on articles where two articles have been combined but the GDFL history is incorrect. The tool is supposed to fix GDFL compliance issues. Yet few administrators are ever taught about the importance of GDFL, history merges, or how to use the tool, potentially leading to many mistakes.
Rollback can be granted to just about anyone by an administrator; rollback was previously regarded as too potentially damaging to articles to give it away. Yet since January, it has been given out to almost anyone who asked for it. The rollback feature is supposed to be used to remove vandalism, but is frequently used in edit wars to quickly "win" article battles. Undo is essentially the same feature.
The watchlist and the many live feed tools are also used to combat vandalism, but can be used to promote "ownership" of articles. Additionally, watchlists of inactive users give a false impression of which articles are being monitored for vandalism at Special:watchlist.
IP block exemption granting was introduced in January of this year. It can be granted to any user in good standing. Yet the tool has attracted little (if any?) notice on WR, despite several WR users (Fozzie, Mercury, and Lar, namely) behind the original proposal.
There are some very nice citation fixing tools which normally appear in the toolbox when a script is added to the user's monobook. They can save hours of work fixing or completing partly incomplete citations. The DOI citation link is one such tool. Yet even this seemingly innocuous tool can damage articles. The tool doesn't (or didn't?) reliably add an appropriate alerting edit summary when automatically tagging a dead link.(link to an example) Adding maintenance tags to articles semi-invisibly (because a flagged bot does the actual edit) without leaving a full edit summary means that articles may get tagged for needing maintenance without alerting anyone that maintenance is even required.