Zoo keeping business isn't a simple task, especially when it get about keeping species from different planets. With intelligent$^1$ creatures you may have conversations and deals, not the case with other creatures, which are most the business because they are 99.9999... % of all creatures, and are the most interesting case because of their diversity, and fewer ethical obligations and easier to fulfill all of them. As being good CII, I assume OP talks about ordinary creatures only.
$\tiny \text{(1) Strongly do not recommend keeping intelligent creatures against their will for exposure. Even God didn't.}$
First of all, you have to understand that this is a complex problem, which you have to solve. Also probably, the first priority isn't entertainment, but the understanding of ecosystems of such planets. In case CII already knows anything possible about ecosystems, there are other ways to implement the system. I suggest one possible solution, considering research and keeping samples is the primary goal. Entertainment is second.
Ecosystem
Build a full replica of each ecosystem for each planet. You may start with simpler tasks by building ecosystems for some regions. Building such systems will enrich knowledge about planet's and their ecosystems, about species and will have scientific value to do, and be more useful in technologies development etc.
Each region ecosystems is one space habitat, so thing, which will divide them is space, and probably for some special cases and as for whole, high temperature, high density, high energy plasma. This will prevent any possibly biological danger of contamination regions between themselves and the star system where they are in.
It will eliminate any possible eruption, the breakthrough of biological samples of any sizes, giga-, mili-, micro-, viruses etc.
Sub habitats
They are for species, and systems where you keep selected samples, in combinations you need or for testing combinations, determine how they affect each other etc. These places are not a replica of original ecosystems, but more places where you design them, refine samples from some diseases, make a selection of them, combine them, make the controllable environment - a lot of things happening there.
Zoo
After testing and refining are done, and you have desired combination you like, you clone that setup to actual exposition. And in that clone setup, ordinary visitors are allowed. If intended or not, they will destroy that composition, you have the backup, and probably a new interesting or not composition.
SmallZoo
Sub habitats are sources of creatures for your captivity content. For those you know is safe to keep that way. At least you will have more control over the level of danger you wish to have.
As a result
A bunch of space habitats, probably hundreds and more per planet, to store and work with. And some exposure habitats.
One 100km diameter habitat, offers plenty of space to clone most of the possible ecosystem regions, but if you need it could be done planet size (by size, but not by mass) As example, some birds travel 12000 km migrations and that travel and distance are important for their species, so you may expect such need like planet size habitat system.
So you will have a set of planet ecosystem, region ecosystem, a bunch of refining testing ecosystems, masterbatch ecosystem, zoo ecosystem, captivity keeping systems.
This way you may have a system of any scale, and for how many planets you like.
A form of habitats is a cylinder, in case if you do not have gravity generators. Axis may be another cylinder, where all transportation system is, places to live, windows for bird high watch, transportation systems direct to the wild, small zoos etc.