I made the same mistake - once - while making the shop cabinets. After that, I decided it was preferable to first insert the dominos into the end grain pieces, then "coax" the sides on with a mallet. One thing is certain, once you have wetted the 5mm dominos with glue (Titebond in my cases) and begin assembling the joints, be sure to drive them all the way home quickly. If you stop even for a short period of time without the joints being fully seated into the edges of the plywood box members, you will greatly increase the likelihood of one of them blowing out through the outside face of the members in which the dominos penetrate a face of the plywood sheet.
Dave R.