yeah, I noticed this issue to.
But it not always failing.
I would advice to set blueValues if you enable autohint to generate binaries.
see the FDK doc and tutorial:
1.5 Using autohint
After the mergeFonts and rotateFont tools are used to generate a CIDFont, there is another very useful tool that can be used, available in AFDKO Version 2.0 or higher, called autohint. The autohint tool can be run on name- and CID-keyed fonts, and uses the hinting parameters—BlueValues array, OtherBlues array, StemSnapH array, StemSnapV array, StdHW, and StdVW—to apply hinting to the CharStrings. You are encouraged to explore its command- line options to determine which are the most appropriate to use.
1.5.1 Calculating Alignment Zones & Stem Width Values
You are strongly encouraged to take great care in calculating the alignment zones and stem width values. The stemHist tool, also included in AFDKO Version 2.0 or higher, is designed to help in calculating alignment zones and stem width values by generating histogram data. The former functionality is invoked using the “-a” command-line option.