Only once did it lead to a benches-clearing altercation and Gaffney walked away from it, preferring the company of former Stanford teammate Jake Stewart, who was playing center field for the Connecticut Tigers at the time.
"The first pitch, you could tell, he threw at me deliberately," Gaffney said. "The next pitch he hit me in the shoulder. While everybody was going at it, I just smiled and went out to talk to Jake."
Gaffney, who will likely see a lot of playing time as a halfback with the Cardinal football team, said getting hit by a pitch is nothing.
"I'd rather get hit by a pitch than get hit by Shayne Skov," he said.
Gaffney is all smiles as he goes through his first full football training camp in two years. He was productive as a baseball player, hitting .297 with an on-base percentage of .483 (he also walked 20 times) and 11 stolen bases. He also missed playing football.
With the blessing of the Pirates organization and following a long talk with his parents, Gaffney went to see Cardinal coach David Shaw about the possibility of returning.
"I talked to my parents in January or February and we took out a whiteboard and wrote out all the pros and cons," Gaffney said. "The essence of it is I could finish my degree, come to play with what is maybe the best team Stanford has ever had and being back in college life as opposed to being on my own."
Gaffney was the No. 2 back behind Stepfan Taylor two years ago, rushing for 455 yards and seven touchdowns on 74 carries. He also caught 12 passes for 79 yards and a touchdown.
It didn't take Shaw very long to bring him back to the fold.
"He always knew that there was going to be an opportunity for him to come back," Shaw said. "I personally thought that he would probably take two years before he made that decision. He played well in baseball; he played really well. I think he missed football. He loves football. When it's all said and done, he's going to play football for pay in the future."
In a perfect world, Gaffney says, he'd like to emulate Deion Sanders and play both sports professionally. He grew up in San Diego, where he'd naturally turn to football in the fall and baseball in the spring.
There are a lot of things he misses about not playing baseball this summer. One thing he won't miss is the 3 1/2 to 10 hour bus rides he'd make in the minors.
"Flying is a lot more luxurious than a 10-hour bus ride," he said. "I still hope to establish myself with the Pirates if that's what I eventually want to do. They were surprised when I told them but very supportive."
Gaffney turned cheerleader for Stanford's run to the Rose Bowl last year and does not regret missing out on the action.
"Watching the season unfold was fun," he said. "Those were my guys out there. I think it's a great experience to see that from the outside."
Gaffney was on schedule to graduate on time when he signed with the Pirates and will need two quarters to complete his degree in sociology and psychology.
On the practice field, after just a few days, his body is a reminder of how he should be feeling, a little sore and weary. It's a feeling that helps unlock his competitive nature and keeps him focused on the daily tasks.
He doesn't feel lost on the football field either. He's been studying the playbook and does not lack for confidence.
"I know what I am doing," Gaffney said. "I hot the playbook pretty hard and we're out here pressing each other pretty hard to be the best we can be."
He also has a good perspective on being a professional rather than an amateur. Baseball become more of a business, a struggle for survival.
"Out here, it's family," Gaffney said. "Everybody is equal here."