I also have this issue. I have two minecarts which run under magma blocks to collect drops from my mob farm. This has been working fine up to version 1.12 but I did notice after the 1.13 update that I lost one minecart. They normally run all the time. Maybe it crossed a chunk boundary during a save and the cart got lost.
on BDS Version 1.13.3.0
Linux ubuntu 4.15.0-66-generic #75-Ubuntu SMP Tue Oct 1 05:24:09 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
have also seen squid dying in one block of water. Bedrock Dedicated Server Version 1.13.0.34
My moving hopper minecarts are disappearing too!