I noticed that a lot of them uses the gothic font, meaning that さ will be written as 2 strokes and not 3.
That may be true, but with the Gothic (sans-serif) font I have always considered the second stroke to be a two-part stroke. So while it's technically only two strokes, I think of it as a character written with three parts.
Do you think this is a potential problem?
No, it's just a font thing. Some fonts will change the characters in different ways, just like you see in English with the various ways to write lowercase letter 'a.' It's just one more thing for a beginning Japanese learner to learn.
Here's another post about font that you may find interesting: Weird usage of dakuten.
If you are a teacher who wants to teach writing hiragana to a beginner, would you prefer an app that doesn't use Gothic font?
I don't think that it matters too much, but most of the learning materials I used to learn Japanese actually favored the Minchô (serif) font. It's not of vital importance what font you use, so long as you are able to recognize the characters involved.
Ultimately, the better you get at reading Japanese, the less various fonts will trip you up. So I would recommend using a clean font to start, and progressing from there. There's no need to hide from the various fonts, because they'll pop up frequently.
That being said, however, since you are writing an app to help learners of the language, I would personally suggest that you use the Minchô font. This is because you will find that most newspapers and books published in Japan use the Minchô font.
You may find this forum post on duolingo interesting as well: Font Choice in App.