A good question. A few comments on this:
1. The duplicate question checker takes word frequency into account, so these common words will contribute much less to whether a question matches, compared to less frequent, identifying words.
2. You can also try adjusting the sensitivity of the duplicate question checker in the admin panel, to reduce false matches. It can also be switched off.
3. You can also adjust the QA_IGNORED_WORDS_FREQ constant towards the bottom of your qa-config.php file - any words which appear more times that this value will be ignored when searching or looking for duplicate questions.
4. If you *really* want to avoid indexing common words, as opposed to these other solutions, you can modify the qa_post_index(...) function in qa-app-post-create.php - after the first three lines, you can add some code which goes over those arrays and removes anything in a list of common words which you create.
5. As a general point, the scoring function for searching (and by extension question matching) could certainly use some improvement, and I plan to address this in a future version.