That’s been normal and expected behavior. I came from org-mode in Emacs as did Tienson (developer), which is what Logseq gained some of its inspiration from. Each time you restart the time tracking feature it’ll log this as a new line entry in the MD file. This line is not a capture of the overall time spent, but it captures the timestamps of when the task went into an active working state and then left that working state. The timestamps are then substracted to get the total duration time for that working session, which then gets applied with the other lines to calculate total time.
The cycling of tasks IMO needs tweaking since it does not always follow that strict flow of “TODO>DOING>DONE”. There is a plugin out on the marketplace that allows you to setup your own custom workflow which may help in your case. The other option if you are not done with a task but need to move it back to the TODO state without cycling through DONE, click on the word “DOING” and that should cycle it back to TODO.
https://writequit.org/denver-emacs/presentations/2017-04-11-time-clocking-with-org.html