What's The Problem?
Logic is unique, defaulting some of its settings to allow for multiple lanes of Automation data to be written (and then overwritten) when certain types MIDI learnable controls are utilised.
For example, using your Mod Wheel to control Timbre, may result in both a MIDI CC1 automation lane and a TIMBRE automation lane to be recorded, as well as data being re-recorded during playback.
How Can I Stop This From Happening (Per Track)?
This can be avoided by clicking the automation state dropdown on your track, and deactivating "Record Automation with MIDI Regions"
How Can I Stop This From Happening (Globally)?
You can alter your default Logic Settings to disallow the recording of Plug-In Automation by entering your Logic Settings, navigating to the Automation tab and deselecting "Plug-In".
Why Is My Automation Data Being Overwritten?
To prevent your carefully crafted automation from being overwritten, please ensure that the default Automation behaviour for your track is set to "Read".
This ensures that the Automation is read and not recorded over.
This can be set by entering your Logic Settings, navigating to the Automation tab and selecting "Read" from the "Write Mode Changes To" dropdown menu.