Are you the member who had suspected that one of them may be pregnant due to some nesting-like behavior? This was maybe a couple weeks ago… Maybe it was someone else?
How confident are you that they are sexed correctly? Are you prepared for separating them (if they are different sexes) by the age of 12 weeks?
Like the others said, you have a couple things working against you, age and the fact that you have multiple buns.
Young bunnies are messy until they catch on to the litterbox, and then they are well-behaved, and then hormones start, and then they are messy again while you wait to spay/neuter. This is in general, of course. Some buns are messy the whole time, some buns are litter-trained the whole time. It really varies…
Having multiple buns may present litter-training issues ALWAYS. This isn’t necessarily a lack of training, but rather territorial marking against each other. Spay/neutering may or may not fix the marking.
A litter-trained bunny is going to pee in the box 100% and poop *mostly* in the box. A dropped poop here or there is common, regardless of whether they are altered and their age.