It depends on what causes the drop.
1. Age : turning an year older after securing ITA and filling eAPR ,and the subsequent drop in CRS is okay
2 .IELTS expiring : once your application is under process,it is alright
3. Any of the experiences that got you the points being disallowed. : Yes,that would be a problem ....if they find your experience which fetched you points is not matching with that of the NOC selected / or the reference letter is not upto their requirements they may reject your that particular experience..in that scenario if the corresponding reduction takes you below the cut off you qualified,there is every chance they your application will get rejected.
example cut off for the draw you got ITA for, was 450 and you had claimed 3 years of experience (50 pts) of which 1 year they refused to accept...now the points will get reduced by 25 and if that would take ur CRS below 450,they will reject your application...
I don't see any other scenario where CRS might come down...