Low eutectic point foods
The eutectic point refers to the melting or freezing temperature of something. Items that need lower temperatures will not easily freeze dry because they don’t easily freeze.
Some of those items include:
- High sugar – Sugar bonds to water, which is actually why it’s good for preserving food. It’s not so good for freeze drying, because it also lowers the freezing point of the food
- High salt – Salt is used to melt snow and ice. It lowers the freezing temperature of water enough to cause issues when you try to freeze dry food with very high salt levels
- Honey – Honey doesn’t actually freeze; it’s a supersaturated solution with only about 18% water [source], and becomes “glassy” between (−44 and −60°F)
- Here’s a cool video that shows how honey becomes glassy on dry ice
- High fructose corn syrup – Like honey, high fructose corn syrup is only about 25% water and doesn’t easily freeze
On a separate note, food that is not completely frozen will boil during the drying stages. Here’s what strawberry puree looked like when we didn’t give the cycle enough time to completely freeze:
The two middle trays didn’t freeze long enough before the dry cycles. 
The trays were also very full; likely close to capacity of the 4-tray freeze dryer. 
The unfrozen puree boiled during the dry cycle, creating an interesting texture.
Food thicknesses
- Thick food takes much longer to dry – The food dries from the outside-in, so thick food takes much longer
- Varying thicknesses – Your cycle will take as long as the thickest item takes to dry
- Overfilling trays – If the trays are filled beyond the freeze dryer’s capacity, you will need to defrost the ice buildup, and continue drying
Other common mistakes
- Raw meats – They are still raw and should not be mixed with cooked items
- Flavors mix – Even in a vacuum, flavors can transfer from one food to another
- Fruit skins – Reduce freeze drying time by puncturing the skin
- High fat – Fat reacts with oxygen and goes rancid
Sources:
http://commonsensehome.com/freeze-drying-mistakes/