hello cousin, as Valerie pointed out, there are some tools to use when there is ambiguity. Endogamy is a fact of life in early days of this province, you should see my tree, starts looking like a spaghetti bowl several generations back.
Take your time connecting upwards, there are a whole lot of profiles already created from the 1750s back to 1600s. Many are indeed products of Gedcom imports where data got lost. Do your research case by case, and if it looks like a duck, quacks like a duck and generally acts like a duck, you are likely to have found the right one, a duck.
Some families are more problematic than others, such as around Lotbinière area, there are Lemay galore there, and other families that intermarry with them a lot. I recall one set I worked on where the husband and wife had identical names to another couple married a few years later in a nearby town. Painstaking research identified the children belonging to each couple, the data got put on profiles so people could see who belonged where. Not much more one can do.