komma ut is a particle verb meaning 'get out of' or 'exit'. You could say Vattnet kommer inte ut ur flaskan meaning 'the water can't get out of the bottle'. But when we're just talking about water flowing from a bottle, we use the simple verb komma. There's no focus on the water exiting [komma ut] the bottle, the focus is on where the water is coming from [komma].
I think what's confusing is that in English, out of is just two prepositions in this case. So that while come out can certainly be a phrasal verbs in some contexts, in a sentence like 'there is water coming out of the bottle', it isn't – it's just two prepositions which together give the same meaning as ur.