Feats and Prerequisites: Certain feats like Arcane Strike (and a lot of prestige classes) rely on the user being able to cast arcane spells - you should consult with your DM on how that would be affected by this.
Magic Items: Certain magic items like incense of meditation specifically mention that the user must be an arcane or divine caster, so you'll need to determine how those items would affect you. Personally, I would rule that incense of meditation doesn't affect you, because that would be really OP on a magus.
Enemy Abilities: Enemies may gain certain advantages against you depending on whether you are an arcane or divine caster. For example, if an antipaladin used Smite Good on you, you might take double smite damage on the first hit like a cleric or paladin would (RAW it just says clerics and paladins, but your GM might rule that it applies).
Other Stuff: As a divine caster, presumably you would technically have orisons as 0th-level spells rather than cantrips. I'm not aware of any mechanics that actually draw a distinction between the two, but it could come up.
While not strictly related to divine spellcasting, your DM may decide that you have the same aura that a cleric or paladin would, and thus are more visible to detect good and may be affected differently by certain spells like righteous blood. Similarly, you could potentially be barred from casting certain spells based on your alignment like clerics are, like summon monster for creatures with certain subtypes.
Story Consequences: Beyond the strict game mechanics, certain regions of Golarion take a dim view of religion and the gods. If your character should ever find himself in one of those places, things could get interesting if his magic is determined to be divine rather than arcane.