In a field outside London, on the 29th of June, 1838, a portal opens up.

[Brother Oni]

Disease is iffy. Their biologies are very different as has been said and ponies tend to be able to command nature as is. Still it is a valid possibility to hurt both sides of the portal.

That's the fun thing about viruses, they tend to be rather non-specific in their hosts.

That's not mentioning parasites or other things that just need water and warmth.

Unless Equestria and all its lifeforms have some really funky biology (for example they're all D-amino acid based life forms), there's going to be something crossing over and when it does, the hosts won't have any specific defences against it, potentially resulting in the scale of deaths when the Europeans went to the Americas.

I agree that this would easily work two ways, but given the state of Victorian England's hygiene (at the time, miasma theory of disease would still be prevalent, with the germ theory of disease still a good number of years away) and the general cleanliness of Equestria, I suspect that more of the Victorian's bugs will be jumping over than Equestria's.