Hello,
Are your pigs newish? When ours were new and shy, they would only stay in one cardboard box in their cage that was also full of hay. They would just eat, poop, wee and sleep in there all day. This was to the extent that we started seeing staining on Marshmallow because he is white.
We changed two things to fix this:
1. a wider variety of hideouts
2. making sure that the hideouts had a good layer of newspaper underneath the base bedding to soak up wee (the poops actually dry out quite quickly if they aren't in a puddle of wee)
Nowadays they are rather more adventurous and they spread their poo and wee freely all over their hutch / run, but I think its quite normal for them to be hiding out in the first weeks.
Not sure if this new pig shyness is the problem you are having, but wanted to make the suggestion in case it helps!