BEIRUT—Signaling a growing rift within Syria's insurgency, al Qaeda-linked militants fighting in the country have killed at least two rebel commanders in the past week, according to several rebel accounts.

Late Friday, activists in the Syrian province of Latakia reported clashes between Free Syrian Army rebels and al Qaeda-linked fighters—two camps battling together against President Bashar al Assad's forces. The clashes came a day after Free Syrian Army military representative Kamal Hamami was gunned down at a rebel checkpoint...