Over the course of about 24 hours I ran into several variations of this situation, and it took me about 25 minutes of staring at my credit card statements to figure out what was going on. In case any of my gentle readers run into a similar situation, I thought I'd share my experience.
Statement credits are treated as discounts, not payments
This is a situation you're bound to run into if you take advantage of Amex Sync deals or Visa Savings Edge. When your statement closes, you won't receive points for the part of your purchase rebated by the two programs.
So if you paid exactly $50 in flowers from 1-800-FLOWERS for Valentine's day and received a $15 Amex Sync rebate (and a 5% Amex OPEN rebate), you'll only earn miles and points on $35 (or $33.25).
Of course that's not true of portal earnings, which your credit card company doesn't see, so you'll receive portal earnings on the entire purchase as reported by the online merchant (who may exclude taxes, shipping, or gift cards, but frequently don't).
Credit card fees aren't treated as purchases
A kind of inverse problem arose when my Chase Sapphire Preferred annual fee hit this month. Since I pay off all my credit cards each month, my statement balance should always equal my purchases during the statement cycle, and I should earn exactly that number of Ultimate Rewards points (plus bonused earnings, which are listed separately).
But this month my numbers were off! Since I'm constantly running experiments with my rewards credit cards, my first thought was that I hadn't earned points for one or more of those small experimental transactions. It wasn't until I realized that I had earned exactly 95 fewer points than I expected that I realized the problem: my $95 annual fee was included in my statement balance, but wasn't treated as a purchase (which, of course, it wasn't).
All this is spelled out in your credit card's terms and conditions, so don't think they're trying to pull a fast one on you. However, it can be confusing the first time you notice it happen. Hopefully after reading this post you'll be both forewarned and forearmed.