Peace be upon you and God's mercy and blessings.
The first person to introduce dots for the purpose of diacritical marks was Abu al-Aswad al-Du'ali, a companion of Amir al-Mu'minin Ali ibn Abi Talib (peace be upon him). He placed a dot before a letter to indicate a Dammah (the vowel sound 'u'), a dot above it for a Fathah (the vowel sound 'a'), and a dot below it for a Kasrah (the vowel sound 'i'). This system remained until al-Khalil ibn Ahmad al-Farahidi came along and established a more precise system. He replaced the dots with a long 'Alif' above the letter for Fathah, a mark below for Kasrah, and a small 'Waw' above for Dammah. He also introduced dots on letters to differentiate and clarify them.
In summary, the first to introduce dots in the Quran was Abu al-Aswad al-Du'ali for the purpose of form and diacritical marks. However, the system of diacritical dots we have today was first established by al-Khalil ibn Ahmad.
There is no issue with this because the primary method of preserving the Quran is through memorization. Many Muslims have memorized the Quran, and the diacritical marks were established based on the widely transmitted recitation. The era in which this occurred is not significant; it is a matter of convention—forms of diacritics and letters—based on an unchanging reality, which is the Quran preserved in the hearts of people.
May you be successful in all good.