1) Just like most standalone touchpads for PCs you may find an urge to lay your PDA flat on a table and just navigate away on your touchpad. A problem with this urge is that pressure you will apply upon the touchpad will most likely move your PDA across the table rather than moving the onscreen cursor.
Example: Lay your bare PDA on a wooden table. Place your finger firmly on the touchscreen. Push your finger.
2) The human finger, sweat/grease, and the slippery touchpad. The touch pad just as a touch screen is not made to be used with greasy hands. The touchpad will get greasy, attract dust, and build up grime. Sometimes resulting in coated less functional areas. If you snack it's even worse. You can see the touchpad get coated with oils you never realised you had on your hands. It builds up. You must clean your touchpad regularly with soap and water.
If you like to eat lunch with your PDA... you'll be using the stylus, not the touchpad.
Example: With PDA powered off. Eat a french fry. Wipe of your fingers with papertowels/napkins/etc. Press finger on screen and slide across. (Alternatively you can stand outside in the hot sun for a few minutes and try the same experiment with sweat)
3) Sensitivity. Touchpads are sensitive. If you brush another finger even along the edge of the touchpad by accident your pointer will move or not function till you figure out a good way to use your touchpad with a single finger.
I might add that popularity of notebooks and the unpopularity of touchpads has spurred a market for micro/travel/wireless mice.