Hi, Normally when creating objects and you have a fill, 4 pens will default be added:
1. Foreground pen
2. Background pen
3. Outline pen (unless it is disabled on your 2D)
4. Pen no. 3
Then another pen will be added for your lines.
Make sure you don't delete the working elements used when creating the objects as you can edit them and replace the existing when needed. I understand that sometimes the pen arrangements when replacing the object becomes different. The only solution that I could think of is to "override" the object pens if this happens.
Hope it helps.