All perfect praise be to Allah, The Lord of the Worlds. I testify that there is none worthy of worship except Allah, and that Muhammad is His slave and Messenger.
This supplication was narrated from the Prophet by many different narrators, and Al-Haythami mentioned it in Al-Majma’ with the following wording:
“May your mother be bereft of you, [this is an expression of condemnation and rebuke] o Abu Bakr; polytheism enters your people more quietly (secretly) than the movement of ants. Shall I not teach you something which if you say will eliminate minor or major (polytheism)?" I replied: Please do, o Prophet of Allah?” He said, "Say every day three times, ‘O Allah! I seek refuge in you lest I associate anything with you while I know it, and I seek your forgiveness for what I do not know.’ Shirk is to say, ‘Allah and so and so gave me, and making an equal is for a man to say: ‘Was it not so-and-so, so and so would have killed me…’”
Then Al-Haythami said after reporting this narration: “It was narrated by Abu Ya’la from the narration of Layth ibn Abu Sulaym, on the authority ofAbu Muhammad, from Hudhayfah. Layth is a Mudalis [definition at bottom of Fatwa].
If Abu Muhammad was the one who narrated from Ibn Mas’ood, and the one who narrated from ‘Uthman ibn ‘Affan, then Ibn Hibban classified him as trustworthy, but if it was another narrator who narrated from other than Ibn Mas’ood and ‘Uthman, then I don’t know him, and the rest of its narrators meet the criteria set by Al-Bukhari and Muslim.
Therefore, there is nothing wrong, Allah willing, in repeating this remembrance three times a day, as it is a good and beautiful supplication.
However, we advise you to repel these whispers, ignore them and not give any attention to them, and know that all your doubts and misapprehensions are pure whispers that are not true. The only way to get rid of them is to repel them and ignore them.
For more benefit on whispers and how to repel them, please refer to Fatawa 174507, 374308 and 356689.
Al Mudalis (المُدلس): It is that a narrator narrates from a Shaykh he met and is known to have narrated from him, but he narrates in this instance, that which he didn’t hear from him directly using wording that gives the impression to the person that he did hear this from him directly).
Allah knows best.