4 months sounds like a long time to be left inside a plastic bag unless the germination was greatly delayed... normally I lift the lid (same as taking the tray out of the bag) as soon as the baby leaves are maybe a quarter inch long, which can be a week or two after germination, depending on the size of the seeds. I usually do it around the time they are growing their first true leaves. The reason I do this is that the longer you leave them under cover, the more opportunity there is for microorganisms to grow in there along with them.
There is always a period of adaptation when you remove the plastic and the baby seedlings have to cope with the soil drying out a bit now and then. So I might mist them with a spray bottle every day or two after removing the plastic, and sort of taper that off over a few weeks until they are getting water twice a week. To reduce the stress on the baby plants, I try to make the transition from total saturation to intermittent saturation as gentle as possible. You definitely do not want to be transplanting them at the same time as this transition. One step at a time.
Baby aloe seedlings can change color for various reasons, so it may not be that easy to sort out why yours are doing it. It may be due to stress (sun, drought, temperature) in which case it can be reversible (within limits of course). Try to figure out if anything has changed in their lives, other than the moisture, since you lifted the lid. And keep them protected from big changes, including in moisture.
They can also turn brown when they are on their way out, in which case the change is irreversible. Sometimes that's due to rot, like spending too long under cover and organisms sprouting in there. Sometimes they just give up because they are under too much stress, which always leaves a bit of a guessing game because you don't know for certain what exactly happened.
Hopefully the color change is temporary and your seedlings will be back to their normal green selves. In the meantime give them some protection and occasional misting and monitor any changes.
