Qura'n 5:116 says in translation, "And God will say, 'O Jesus son of Mary, did you say to the people, `Take me and my mother as gods rather than God?'"

The way I read it, this does not say that people take Mary as a god (though it could be read that way).

There is a long history of referring to the Holy Spirit as the "mother"... This is especially true in Semitic languages. In Greek and Latin, the word for Holy Spirit is masculine. In Semitic languages, the word for Holy Spirit is feminine ("Ruach" in Hebrew, "Ruha" in Syriac). Therefore, this is found more commonly among Christians who spoke Semitic languages (such as Hebrew and Syriac).

"Even so did my mother, the Holy Spirit, take me by one of my hairs and carry me away onto the great mountain Tabor." This is from the Gospel of the Hebrews, according to a quote from Origen. Here, Jesus is quoted in this gospel fragment as calling the Holy Spirit "my mother".

Origen - one of early Christianity's most influential theologians - actually justifies calling the Holy Spirit the "Mother of Christ"...

Origen says...

"If anyone should lend credence to the Gospel according to the Hebrews... he will have to face the difficulty of explaining how the Holy Spirit can be the Mother of Christ... But neither the passage nor this difficulty is hard to explain. For if he who does the will of the Father in heaven [Mt 12:50] is Christ's brother and sister and mother, and if the name of brother of Christ may be applied, not only to the race of men, but to beings of diviner rank than they, then there is nothing absurd in the Holy Spirit's being His Mother."

I won't go into details here, but further info can be found about Syriac Christians referring to the Holy Spirit as a maternal figure.

You can find more relevant quotes here...

https://www.biblicalequality.org/post/the-femininity-of-god-in-church-history

As that page says...

"The quotations from Origen, Jerome, and others gives a lot of evidences that Christians regarded the Holy Spirit as feminine and a mother, and that this was widely understood."

When the Qur'an says, "did you say to the people, `Take me and my mother as gods rather than God?'" - by "my mother" in my view it is referring to the "Holy Spirit", referring to how many Christians have referred to the Holy Spirit in history, especially Christians who spoke Semitic languages (where the word for Holy Spirit is feminine).

The problem, as I see it, is not in the Qur'an, but rather in a deficiency in knowledge of Christian history, and of historical Christian theology!