This video from NASA shows Jeff Williams entering BEAM for the first time. He's wearing a simple dust mask. Why is that? If there is concern about floating particles, wouldn't there be a concern with leaving the hatch ajar?
The planetary society had a nice article on this: http://www.planetary.org/blogs/jason-davis/2016/20160606-first-look-in-beam.html
Williams and Skripochka wore face masks as they entered, which is standard procedure for initial inspections of cargo ships visiting the station.
They also wear the masks when they add a new module to the station. Less so now, with assembly mostly complete.
On Earth, when they are packed, all sorts of stuff settles, no matter how clean-room an approach is taken. During launch lots of disturbances in the Force (gravity forces) occur, and stuff gets shaken around a lot, and they are unsure what will be in their faces when they open it.