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Maybe he's angry that "she has a headache". Females often get cranky and growl at her mate because her hormone levels are changing ...perhaps this is just his response because of that or because she's ignoring him. Unless it gets nasty,should be safe to leave together for the 1st 6 weeks if the dogs are not left alone.

Usually it's best that they be separated for the 3rd trimester (6-9 week period), and better to keep them apart till the litter is weaned,especially if he's not up to date on vaccinations and you don't want her pregnant again.
 
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