Here is the scenario you've presented.
- User 1 answered a question
- User 2 found a possible duplicate
- User 1 agreed that it is a duplicate
Is User 1 misusing the system? TL;DR No, they are not misusing the system.
Regarding the first point, User 1 is not required to search for duplicates before answering. (Is it my responsibility to search for duplicates & vote to close before answering?)
Unless you recall a specific question that you think is a duplicate, it's not an expectation that you do exhaustive searching to look for a duplicate.
Regarding the last point, it's been established that answering and voting to close are distinct things. (Should a user be allowed to vote to close a question that he has answered?)
To that end, I see answering and voting to close as two separate and distinct actions.
Because User 1 was not aware of the possible duplicate, User 1 answered. User 1 became aware of said post, User 1 voted as they saw fit.
User 1 has nothing to gain from said actions above. On the contrary, if they voted leave open, one could allege (without proof) that they want fresh fake internet points, especially if a question hits the hot network questions list.