As mentioned here ( EGS Recycle Structures ) You will only get 90% of the parts back from a recycle. There is no guarantee that of that 90% you will get your alien core back. Also, you may want to include a little more information. Was your backpack full? was your OCD full? That can also stop it from returning.
“Depending on your upgrade level for EGS Recycle, you will be able to recycle vessels and get up to 90% of your materials back, and perform recycles at a number of locations, and possibly anywhere , if your EGS Recycle level is high enough.”