Generally we create plan guide or query hints to improve the performance of the query, but some times it would create problems if not used carefully.

To identify if the query is using plan guide look at the planguidedb attribute in XML plan. Sys.Plan_guides will also have an entry.
Query hints can be identifies by looking at the query.We will see hints like opton (force order),Inner loop join, index = etc
If you are tunning a slow query and if it is using plan guides or query hints first remove the hints and tune the query normally