A-spec points can only be won once. Once you win the maximum amount, you cannot win any more from that race. The only way to win more is if you, say, do a race for 56pts, and race it again for 94pts. The second time around, you will win 38pts (94-56=38) for the grand total of 90 points. Once you get to 200 (250 for missions) you maxed them out for that race.
I don't know why the "mission cleared" is cleared, as I've never repeated missions, but as long as you keep the .2% game completion for each, I wouldn't worry. The percentage, not the message, is the important part.