Due to a problem in the Quartus® Prime Pro Edition Software version 18.1 and earlier, the signals in the Signal Tap Logic Analyzer may be displayed in red, even though they are actually connected to the internal nodes during compilation.
To check whether the signals in the Signal Tap Logic Analyzer are correctly connected, go to the Compilation Report > Synthesis folder > In-System Debugging report. The actual connection column reports the real connection after compilation.
This problem is fixed starting with the Quartus® Prime Pro Edition Software version 19.3.