What Can Be Used to Fill in Missing Teeth in the Invisalign Trays?

This is possible, most dentist and orthodontist use white filling material to fill up a missing tooth. It can come off but all you need to do is to take it back again to the dentist and they will do it for you. This will not harm your Invisalign trays and will look great!

It sounds like your orthodontist has put some tooth colored material into the aligner to fill the space.  The aligners themselves have a tooth shaped space for this, so it should be easy to continue to do this as you progress through the aligners.  It will be easiest if whatever is used can be transferred from one aligner to the next.  Also, the location of the missing teeth in your mouth is a factor: if they are in the back they aren't very visible, so s material that is just tooth colored will work, but if they are in the front a denture tooth will look better. 

We have used denture teeth, even matching with an ideal shade, successfully with a missing tooth when doing Invisalign treatment.  You will only need one tooth for each missing tooth as the tooth can successfully be transferred from aligner to aligner if it is not cemented to the aligner.  If your orthodontist doesn't have any denture teeth,  they can order them, or your family dentist also could get them.  They will have to be altered to eliminate impinging on the gums before you can use them.

Ask for some tooth colored wax to fill the space!  works well and it is easy to do on multiple aligners rather than having to preopen and glue in a missing teeth for every aligner

A simple solution is to use denture teeth inserted into the aligners.  This can be challenging at first, but can work well.  Another option is to bond in some filling material into the space, and one patient of mine put the end of a q-tip in the spot and was satisfied.

SOMETHING can be done for you.