Sorry you didn't get all your STB air miles. I don't think using 2 or more coupons in one trip/purchase would make the difference. On both accounts (mine & my husband's) I used at least 2 coupons in one transaction and I believe once I used 4 coupons. Both of us received the 2,000 bonus miles.
I just checked the coupons I used and they were the Shell spend $50, Rexall spend $25, Rosa taco kit, 3 chocolate bars, 2 herbal essence hair products, 3 chocolate bars again, rosa taco kit again, and Sobey's spend $100 get 60. All of my STB coupons posted in November.
On my husband's card I used the Shell spend $50, Staples spend $75 for 25, two of the Rosa taco kits, two of the chocolate bars and the 2 herbal essence hair products. All his STB coupons posted in December.
Hope this helps you narrow it down. If you received the bonus air miles for all the coupons you used, I suggest "chatting" with them to get your full bonus miles. Do you still have the receipts?