This area of halacha can indeed feel confusing and counterintuitive. We hope we can help clarify it somewhat by reviewing the sources of the laws of stains.
On the level of Torah law (d’oraita), uterine bleeding that is not accompanied by a hargashah (halachic sensation indicating the onset of menses) does not render a woman niddah. The laws of ketamim (stains) were enacted as a rabbinic stringency (d’rabbanan) on Torah law. Thus, under certain circumstances, bleeding or staining without hargashah will render a woman niddah according to rabbinic law.
When formulating the laws of ketamim, the Sages built in a set of leniencies that allow for a normal marital life, which is also an important halachic consideration. There is no need to feel uneasy with following halacha properly – both in its stringencies and its leniencies – remembering that they were both instituted by the same halachic authorities.
Staining that one does not notice is not subject to the stringencies of the laws of ketamim. Further, the Sages did not require a woman to look for staining or bleeding unless she experiences a hargashah or an actual flow, or during her shivah neki’im or on an onah day. Therefore, it is completely legitimate to avoid looking.
Toilet paper is a surface that is not susceptible to ritual impurity (tum’ah), so in theory stains on toilet paper may be disregarded. However, accoriding to Ashkenazi halachic rulings, if one wiped within a few seconds of urinating, there is a concern that the sensation of urination masked a hargashah, so we are strict with stains on toilet paper if one wiped immedeiately urinating. According to Sephardi halachic rulings, stains on toilet paper do not render a woman niddah even if found immediately after urinating. Please see our pages on Stains and Toilet Paper for detailed discussion of these halachot.
Even if you are Ashkenazi, as long as you take care to wait a few seconds (ideally 15 seconds) after urinating before wiping, stains on toilet paper may be disregarded and do not render you niddah.
Additionally, if you do find staining (in a manner that does not render you niddah), we recommend abstaining until about 24 hours after staining has subsided so your status may be fully clarified. This is a precaution, not a halachic requirement.
Please feel free to get back to us with any further questions.
This response has been updated to reflect the rulings of our current Rabbinic Supervisor, Rav Kenneth Auman, regarding waiting before wiping.