A lot of snakes don't like their heads touched, but ball pythons especially tend to be pretty head shy. It's just their natural reaction to pull away from anything poking at their face. If you need to check out something near their head/neck, you can usually manipulate them around or gently hold them in place for a second or two. Slow movements are always the best when you're working around their face. It can be frustrating, but as with everything else with ball pythons, patience and persistence are virtues.
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