Second appraisals can be ordered for a variety of reasons. If you are not being asked to pay for it, I wouldn't worry about it. Here ar a couple of reasons:
(1) The appraiser that was used did not do a good job or was black listd by the particular lender. This means that the lender may not be acceptable to the lender with whom you made your application. The appraiser may have been approved at the time the appraisal was ordered but was taken off the bank's list of approved appraisers for some reason. The reason could be totally unrelated to your loan.
(2) You applied with a mortgage broker who must "shop" your loan in order to get it approved. Or, the mortgage broker wants to change lenders for another reason and the first appraisal cannot be assigned to the new lender.
(3) You changed mortgage programs and the program you changed to required a different underwriter and a different appraisal.
(4) The underwriter was unhappy with the appraisal, the comparables used or something with the first appraisal that was wrong. The appraisal failed the computerized evaluation and caused concern in the mind of the underwriter.
(5) The property is valued at an amount that requires a second appraisal. I have seen this on expensive home sales, sometimes multi-family houses.
(6) There was a material change in your qualifications and you are purchasing a multi-family home and using rental income for qualification purposes.
(7) Some other reason that I do not know. Lenders always come up with something new.
If you are concerned, speak to your loan officer and/or the lender directly. They should tell you what is going on and whether you ought to be concerned. You can always run the entire process by your attorney who could possibly give you more advice and guidance.