The FedEx integration is great to have but also a little spartan.
If you are shipping very small items the following will probably not affect you.
However, if you are shipping items 3 or more pounds in weight and using packaging larger than 6x6x6 inches you almost certainly need to deal with dimensional weight when calculating shipping.
Dimensional weight is what carriers now use in many instances instead of actual weight, Through the use of a simple formula applied against the dimensions of your packaging they compare the results of that formula to the actual weight of your package. And naturally, they use the greater of the two.
For 5 pounds shipped in a 12x12x12 inch box, for ground services it is priced at weight - so five pounds. Unless your package is very large in actual size, for ground service you won't likely trigger dimensional weight.
However, all customer packaged express shipments use the larger of either actual weight or the dimensional weight.
For FedEx the formula is your package dimensions multiplied together divided by 166. Using my 12x12x12 box that results in a dimensional weight of 10 pounds. Also note that the divisor used to be 190-ish; they dropped that number recently triggering more instances of dimensional weight trumping actual package weight. Wouldn't be surprised if this trend continues...
Since packages in Nexus just have a single weight setting, this is all that gets passed to the FedEx api for calculating shipping charges.
If I let people choose between ground and express I have to either list the item at 5 pounds and eat the overages I'd get with those that choose express. Go with 10 and stick it to the those that go with ground. Or split the difference.
Naturally if there are both domestic and international purchases based on the same package things can get ugly. The more expensive a shipping option is, the more the real charges will vary from what Nexus provides.
You can hack this problem now by having separate packages for domestic and international purchases but that's duplication of effort, more clutter in the storefront, etc. Another "fix" would be to just have duplicate items and restrict shipping options to one choice and setting the weight as needed to get the correct amount.
Note that UPS does the same thing so if they are added as a shipping feature in a future version of Nexus this problem will remain.
FedEx may not reweigh everything you ship but it can and will happen and you will be billed the difference if you are under.