Based on your description, that you saw what looked like a brown thread from the towel after tevilah, there is no cause for halachic concern.
There are many women like you, who find themselves frustrated and worried by concerns that they have found something that invalidated their immersion. In many cases there is no halachic cause for concern, since common sense explanations such as you provide can be relied on. Additionally, the halachot regarding preparation for mikveh already build in a number of stringencies, so that a woman who makes a real effort to prepare for immersion will generally have one that is valid.
All that being said, if you find these concerns recurring month after month, you might benefit from speaking with a counselor who can help you learn to cope with them. It is understandable that IVF has created real stress for you. That is something else with which a professional may be able to help. Referrals to religious therapists can be found at nefesh.org or www.gethelpisrael.com.
For halachic guidance on matters related to halacha and fertility treatments, we invite you to a schedule a free consultation with a Yoetzet Halacha Fertility Counselor, details here.
Please let us know if we can be of further assistance.
2024: For more extensive discussion, please see our our article on OCD and Niddah, and our brochure “What are you feeling?!” on mikveh stress.