Most of the way through the film, they seem to have used a female doggy. However, there are a few places (for example, the end when they are playing as a family) where it's a little obvious that it's a male doggy.
That's how most movies involving animals are made. People train more than one "identical" animal for different purposes. It's too bad the difference is noticeable, but give them a break!
It can't be that hard to find a doggy-double of the same gender. Especially when beagles seldom differ in markings.
It's also not unheard of to "dress up" a female dog to look like a male. This could easily have been done here.
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