Did you attach your accounts with the tax return? I attach my accounts along with PRCs in one PDF document before submitting return.
Although attaching accounts is not required, but its better to attach it in case of availing tax exemption.
If you think everything in fine, tax returns are correct and you have proof (PRCs). Then ignore this notice, as it could be automated based on spending vs tax paid without taking into account the tax exemptions. But since you're under the radar, be prepared to get audited in future, especially if you didn't attach tax exemption proof.