It's not unusual to tense up and be self-conscious when you first start wearing a hak. It does require some getting used to. The added tension can certainly affect the way your body impacts the mat, and if the koshita is too firm, this could add to your discomfort. There are hakama styles available that are more suited to ukemi than some of those that are used in the non-falling arts, such as kendo or iaido. Suggest you visit the bujindesign.com
website for some good info on the hakama.
One other factor that may be affecting you is that you may now be wearing your obi in a different bearing, now that the hak is in play. This could also be causing you to roll over things in a different way as you take your falls. Try to relax as much as possible, and take "quiet" ukemi. Your body will most likely adjust if given a bit of time and patience, but continued significant bruising is a sign that your uni has a fitment or construction issue of the nature I described above.