It's possible that it could be due to an irregularity in your cycle related to hormones. Your medical practitioner will have a way to test for hormonal levels.

According to Dr. Karen Rosewater, some irregular bleeding may also occur as a result of yeast or bacterial infections or sexually transmitted diseases, such as chlamydia and gonorrhea. But these STDs are usually associated with pain, and you're less likely to have picked one up if you've faithfully used condoms. Irregular bleeding can sometimes occur during the implantation stage in pregnancy, which is also unlikely if you've been really careful when using condoms.

These are just a few examples in the range of possible causes. To pinpoint your specific issue, I would recommend that you consult a medical practitioner who can pursue a thorough diagnosis and plan for treatment, if one is needed.

Take care.