When you travel under the Visa Waiver Program (which most people call "using an ESTA"), you get an I-94 when you enter the US, which specifies an end date, normally 90 days later.
Normally, if you exit the US and come back later, you get a new I-94, with 90 days from the new admission (but there are caveats, see below).
However, when you travel for a short duration to neighbouring countries (Mexico, Canada) and adjacent islands (islands of the Caribbean) and come back before the end of the I-94, you get re-admitted under the original I-94. It's as if you had never left the US: you get the 90 days originally granted, and not more.
So no, there is no problem with that.
The issue your wife may have heard of is about people thinking they can get 90 days, travel to Canada shortly before the end of those 90 days, come back, and get 90 more days nearly consecutively (a so-called "visa run"). This usually doesn't work:
- If one comes back before the 90 days are over, they are likely to grant you only the remaining days of the original I-94 (they can grant a new I-94 if they want, with either the full 90 days or only a few days, but that's their decision)
- If one comes back after that, they are likely to refuse entry, or allow only a few days, as you are not supposed to use successive or repeated visits to live in the US. The usual rule of thumb of that is that you need to stay out about as much as you stayed in.
In your case, as long as your total trip (US + Canada + US) stays within the regular 90 days, there is no issue at all.
Note however that if you travel to Canada by plane, you will need a Canadian eTA.