The compound(s) that have exactly three stereoisomers in total (enantiomers counted separately, and meso forms counted as one) is(are)

Count each case. 1,3-Dimethylcyclohexane has two stereocentres with identical substituents: the $cis$ isomer is meso (it has a mirror plane) and the $trans$ isomer exists as a pair of enantiomers, giving $1+2=3$ (A is correct). 1,2-Dimethylcyclohexane behaves the same way: $cis$ is meso (flipping chair forms interconvert) and $trans$ is chiral as an enantiomeric pair, total 3 (B is correct). 2,3-Dichloropentane has two stereocentres bearing different end groups ($\mathrm{CH_3}$ and $\mathrm{C_2H_5}$), so there is no meso form and the total is $2^2=4$ (C is wrong). Hexa-2,4-diene has two stereogenic double bonds with identical ends, so $EE$, $ZZ$ and $EZ$ exist, and $EZ=ZE$, giving 3 (D is correct).