Having read the first 3 volumes of Negi, it gets edgier. No outright nudity (where it 'should' happen, it's Akamatsufied), but there's one scene where Negi's students get him in the bath and out of his clothes (against his wishes), which is kind of risque (quote 'Let's make it get bigger!'...'But he's only 11; I don't think it will!'...'Well, why wouldn't it?'

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I think it's not so much the display of nudity but the implication thereof, the frequency thereof, and the ages of the 'victims' which is the issue.
The Taiwanese edition carries the same warning label - I don't think it did for vol. 1, but 2 onwards have them.