Could malt used in bread show up as dark brown "grains" in the finished loaf?
Without pictures, it's hard to say for sure, but that doesn't sound like malt. Malt syrup (barley being the standard grain used for malt) is fairly dark (between honey and molasses in color), but it's also transparent and would be dissolved in the dough. Malt powder isn't significantly darker than flour, and should be distributed evenly through the other dry ingredients. Neither are used as a "darkening agent", aside from occasionally being used to darken the crust of bread slightly. As rumtscho points out in the comments, there is a "rye malt" which is used as a darkening agent in some traditional breads. If this is used, it could be a lump that didn't get mixed in? A much more common darkening agent would be caramel color, which is still very unlikely to lead to dark lumps, as it dissolves easily in water. 

Depending on the type of bread, it could be a kernel of some type of grain (rye maybe?) or a lump of unhydrated flour. Without more details, there's no way to give a definite answer, but it doesn't sound like malt.