Had one board that way. Think it was from near surface of log. Tended to have flakes pop up. If this is the case, then only solution I know of is to replace board. Regular boards should not splinter. Have you pressure washed deck? Incorrect pressure washing can damage surface, fraying top layer(need to set for wide stream and keep tip few inches away from deck). IPE being hard, small splinters can penetrate even if very thin. If this is the case, need to sand deck.

After one year of weathering, sometimes Ipe is a little splintery. A 5" orbital sander with 50 grit coarse sanding discs is the easiest way to remove those little splinters.