I don't necessarily disagree with your assessment. In fact you are probably entirely correct that these were individual captures. However, I would like to draw your attention to a couple of things.
First, my memory may be playing tricks on me, but I am remembering reading about a [wagon? railway?] train that was captured by the Confederates that was carrying a large quantity of M1849s. I don't remember the date or location.
Secondly, while the M1849 may not have been the most issued weapon by the Union, there were 17,000 of them bought by the U.S. during the Civil War. That is the same number as .36 caliber Colt Navys bought, and over 10% of all Colts bought by the Union. More were probably bought by the individual northern States, too. Larger size shipments would not be improbable.
You mention the Matamoros shipments. Also of note are the Brownsville, Texas shipments. According to a communiqué dated March 1863 by Gen. Bee, Colts could be shipped from New York to Brownsville without problems. Cost was $25 for Navy caliber and $38 for Army caliber.