Ugo Monye and Tommy Bowe had tries ruled out in the first period, while Mike Phillips and Monye again came within inches of adding to the Lions' tally during an incredible second-half comeback.
"There were good scoring chances that we didn't take. If we had we, could have been comfortably in front," said McGeechan, who watched his side repeatedly cross the gain line out wide and in midfield at the ABSA Stadium.
"In the end, we scored two tries in the second half, but missed three or four others.
"To have 60-per-cent territory against the Springboks in South Africa is unusual and we didn't make the most of it.
"But to come back in the manner we did was very pleasing. We had two or three scoring chances in the first half and only took one of them. But we had the confidence to keep playing.
"The disappointment overall comes from the fact that we played so well. Some of the rugby we were playing was outstanding."