Firstly, they would definitely have noticed if they had strange cattle in the milking herd, even if they were dairy cows. We have 300 but any of us, except the work experience kid, would know if we had a strange cow in the parlour.
So, that probably means the infection has come from the cattle getting out. I would have thought Bridge farm would vaccinate against IBR (all the Archers do things by the book, don't they!) But didn't Ed put another escaped group in with some cattle at Home farm? On the herbal leys? So maybe those cattle infected the Brookfield cows.
I think it's unlikely to be Josh's fault mainly because he seems to avoid working with the cows wherever possible! And to be honest I'd have thought when he was visiting other farms he'd be in fairly smart clothes, rather than working clothes.
But no doubt there is supposed some conflict caused by Pip and Josh blaming each other. Maybe it wont be either of them!
Oh, and beef cows don't get milked because they feed their own calves. They do have a calf every year though - in case anyone thinks they are culled after reading one calf.