Well, it could be a problem.
One of my friends ("Bill") took his initial CFI checkride with the FSDO... Went in as a commercial pilot, came out with a private ticket. The FAA inspector who reviewed his logbook realized that Bill hadn't met the requirements for the commercial. In particular, Bill and his instructor had omitted the day and night dual VFR cross-country flights. The examiner who gave Bill his commercial checkride should have picked up on this, but didn't. (Note: The aeronautical experience requirements had changed just a few weeks before Bill took his commercial checkride, which partially explains how Bill's highly experienced instructor could have made this mistake.)
Fortunately, the inspector was a pretty reasonable guy, so he re-issued Bill a private ticket and told Bill and his instructor to go "fix" the problem. After completing his dual VFR cross-country flights and getting his commercial certificate back, Bill re-took his CFI (with the same inspector) and passed with flying colors.
The guy that really got in hot water here was Bill's examiner for the commercial (and to a lesser extent, Bill's instructor). Again, the FAA inspector was able to solve this problem in a constructive way. The CFI and DPE got a pretty major @ss-chewing, but I don't think there were any other long-term repercussions.
If you are really concerned about this, start by talking with your instructor.
FFFI