Arena slammed the MLS in August for alleged interference in the Galaxy's attempt to sign American midfielder Sacha Kljestan from Anderlecht.
The 62-year-old and former United States boss claimed "forces within the league worked real hard to make sure that didn't happen."
When asked why the MLS would interfere, Arena responded: "Because they are children and there have to be adults in the process, and we didn't have enough of them.
"I think we are back into the old days in the league when the rules are somewhat arbitrary. Hopefully we will get that straightened out in the off-season."
On Thursday, MLS commissioner Don Garber said he was hesitant to sanction Arena.
"It pains me to have to fine [Arena] for making comments that he obviously feels strongly about, but which he is required by league rules to keep to himself," Garber said.
Arena did not back down, after learning of his penalty.
"I've got no thoughts on what he has to say. I stand on everything that we did as completely accurate and completely ethical," Arena said.
"It was the way that you do things - the right way. We did everything the right way and we'll leave it at that.
"We stand by everything that we did and I'm very proud of our organisation with the way that we go about doing our business."