It’s possible this is related to “Replace newlines with HTML” in AnkiDroid [Settings > Advanced]. It’s hard to know whether to call this a feature, or a bug, or a workaround – I guess, beauty is in the eye of the beholder. For some users’ workflows, this setting gives them something they want – for some (especially when editing happens on multiple platforms), this causes unexpected gaps in their fields.
See if these posts and examples look familiar to you. Some of the suggestions there might help you find a way to get more consistent behavior across platforms without any change to the code.
I think the work that is already underway to bring the editor interfaces closer together – like integrating the desktop editor into AnkiMobile and updating the AnkiDroid editor – will make these distinctions moot, or at least less noticeable.
If this isn’t related to what you’re seeing and I’ve missed the mark – it might help if you can show an example of a note you have where the HTML looks different on desktop vs. AnkiDroid vs. AnkiMobile – after it is saved and synced.
For some users’ workflows, this setting gives them something they want – for some (especially when editing happens on multiple platforms), this causes unexpected gaps in their fields.