A 37-20 defeat at the hands of the Llanelli Scarlets in Round 13 left Munster eight points off the pace, although leaders Ulster had to be content with a losing bonus point after being pipped by Glasgow Rugby.
"Obviously having seven players with the Irish squad is having an impact," said Gaffney. "But we could live with that if we did not have so many quality players out with long term injuries - that is what is hitting us so hard.
"Having players like Christian Cullen, Marcus Horan, Alan Quinlan, David Wallace and Jeremy Staunton absent injured is what has made it so difficult.
"But while I was not that disappointed with the performance at Stradey Park what I was disappointed with was not to come away with something.
"They were the better side and did put us away very clinically but I felt we did enough to get out of it with a bonus point for a fourth try - and possibly even a couple of bonus points instead of nothing."
Now they face another Welsh challenge with the Neath-Swansea Ospreys travelling to Musgrave Park in search of the season's double with Gaffney wary of the danger Gavin Henson poses with both the boot and ball on hand.
"The Ospreys like to run the ball - and they are pretty good at doing it," said Gaffney. "They beat us at St Helens when Henson kicked everything in sight while we virtually didn't kick anything at all.
"They are a good side with a very attacking backline. Players like Henson, Dave Tiueti and Shaun Connor are always capable of posing problems."