The behavior the OP reports is not normal, nor have I personally experienced it, but sometimes Obsidian doesn’t behave normally. I suggest creating a small test vault, without any community plugins but with the same settings for Core Plugins as your working vault. Index the test vault in DEVONthink and see if you can reproduce the error. If no, that will indicate the error is probably in Obsidian, and possibly with a community plugin.
In your production vault you can turn off plugins and then turn them on until the problem reoccurs. I know there are cases, e.g., the “File Tree Alternative” community plugin, which have settings for trashed documents that can vary from the setting in the “Files and Links” core plugin.
(Also, though it’s not cheap, Obsidian Sync service is able to manage trashes across all devices. Just saying.)