I could see a couple of possibilities. If you have anti-virus scanning your recordings folder, it could place a lock on the file while at the same time 3CX is trying to write to the file. In the case of recordings, 3CX will create the initial file and continue to write to the file as the phone call continues. If 3CX cannot write to the file, it seems plausible that you could miss some of the conversation.
Another possibility is that you ran out of resources on the 3CX server. Things like anti-virus scans, windows updates, running of highly complex reports, transcoding audio, etc. could consume a significant amount of resources and potentially impact the recording of phone calls. If you can reproduce the issue, what are the available resources (CPU/RAM) at the time?
I've been implementing 3CX for nearly 20 years and have never seen this issue before.. but I always ensure the 3CX server has more than sufficient resources to run. And if I run anti-virus, I make sure it doe not scan any of the 3CX folders.
Question -- where is 3CX saving the recordings? On a local disk, a NAS, a network shared folder? 3CX must be writing the original recording on local drives. You can archive it elsewhere, but the original recording must be local, and typically on high-speed drives. The speed of the drives is less important for an 8SC license, but the more simultaneous recordings, the more important the speed of the hard drives become.
Is you 3CX server on Windows or Linux? Windows is pretty picky about file locks, while Linux is more forgiving.