Here are the rules for super visa:
(1) NOA exceeds LICO, or
(2) You income within recently 12 month exceeds LICO.
If you only worked for 3 months, you income is only around 3 W $. I guess, you passed the first round screening, which is easier, and get the medical examination done. but you failed at the second VO, when he double checked your file.
You medical examination will expired within 1 year. So, if you can re-apply within one year, you do not need to do it again.
By the way, whether your company is goverment or large company, and whether your job is permanent or contract also matters.