There are lots of things that could be going wrong, but more info is needed...for example:
...are you preheating the oven well before putting the clay in
...what size oven are you using
...do you have the thermometer in nearly the same place as the clay
...how did you calibrate your thermometer
...what brand, and line, of polymer clay are you using
...what size, and what shape is your clay piece, and how thin at the thickest area, and does it have projections
...what position in the oven is your oven shelf
...what baking surface(s) are you using...some will heat up hotter than the heated air temp
...do you have anything else on the clay
...what temperature are you using
...how long are you baking
Btw, polymer clay isn't generally completely covered when baking, although that could be done to even out the temperature reaching all parts of the clay--if doing that though, the foil or other material, etc, does not generally touch the clay**.
If using metal foil, it's usually "tented" over the clay item, or a box could be inverted over the clay, or the clay could be inside a plastic roasting bag which will balloon in the heat, etc. Damp paper towels can be draped directly over the clay, and the clay can be in direct contact with materials that won't leave marks like wadded tissues or cotton fabric, polyester stuffing, etc, or the clay can be sitting on or in a pile of baking soda or cornstarch, etc, etc.
You might want to check out my page on baking polymer clay too for more details:http://glassattic.com/polymer/baking.htm
** and very smooth materials like aluminum foil (or glass or other metals) will leave shiny spots on the clay anyway wherever it touches