Is there any disadvantage to having PhD skipping M.Sc.? In some countries like Australia, Singapore etc, A candidate may be enrolled into Masters leading to PhD program on condition that he/she will pass the candidature test after the 1st year and are subsequently given PhD in the final/fourth year (subject to successful completion), which results in no M.Sc. degree in between.

Is there any discrepancy towards these PhD holder in academic or professional life?
No.  Once you have a PhD, nobody cares about your previous degrees, or if you even graduated from high school.

(I know at least one tenured professor who did not graduate from high school.)