This is not a bug.
In four dimensions the difference is zero, by use of the Schouten identity.
That R4 is not zero in D dimensions is a consequence of the way the trace is calculated. This is in general dependent on the "gamma5-prescription". It is up to the user to determine how to do these kind of traces (e.g., by determining where to put gamma5 in Tr, this can be hairy and you might have to worry about anomalies etc.).
In:= << "HighEnergyPhysics`fc`"
Loading FeynCalc from /home/rolfm/HighEnergyPhysics
FeynCalc 8.0.0.beta2 Type ?FeynCalc for help or visit http://www.feyncalc.org/
$PrePrint is set to FeynCalcForm. Use FI and FC to change the display format.
Loading FeynArts, see www.feynarts.de for documentation
FeynArts 3.4 patched for use with FeynCalc
In:= (R = Simplify[Tr[GAD[a, b, c, d, 5, e, f]]];
R2 = DiracSimplify[GAD[a, b, c, d, 5, e, f]];
R3 = Simplify[Tr[R2]];R4 = Simplify[R - R3];
Schouten[R4 /. D -> 4])
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