Maybe related to this? macOS 10.13.4 Freezing with BetterTouchTool Usage
In the case of the linked issue, there are system/input freezes for 15+ seconds at a time whenever an app switch occurs (eg clicking on the window of another app, or cmd-tab to another app, etc.) Closing BTT resolves the issue for a while.
All of us reporting in the linked thread are using Magic Trackpads and/or other USB input devices.