You're refering to viewing them in your LW Library window right? There's a couple of possible reasons. Firstly, when you 1st open LW, all shared & incomplete files will be red until LW can account for them (you can watch as your shared files tally adds up; eg: 235/500.) As LW accounts for them they will turn from red to black. Incompletes are last on the list. The second reason is when the incomplete file loses its relationship with its counterpart in the dwnld window. This can happen if (for some odd reason) the dwnld file connects with a different source & it creates a 2nd incomplete file. Another reason is if you have deleted the item from the dwnld window but its counterpart in the incomplete folder still exists. More on this can be read here (my 1st post on the forum):
Library Items in Red.