Are you buying a short sale? If the house ws appraised over 6 months ago, the bank will need a current appraisal for your offer.
If you are using FHA loan, there is sometimes a second appraisal done, in addition to the one your lender orders.
Lenders use AVM's - Automated Valuation Methods - a mathematical computation to estimate the value of a property. AVMs can be widely erroneous, and lenders know this. When an AVM and an onsite appraised value differ greatly, a second appraisal may be requested. It is not an automatic assumption that the onsite appraisal was incorrect. The two simply had a difference exceeding the lender's tolerance. The solution is to seek another appraisal and compare.
My example above is only one possibility. There may be several others.
The request is not an automatic 'problem' - so don't worry needlessly. While it can be discomforting, don't over alarm yourself. They will let you know if there is a concern. Until then, proceed optimistically.
This isn't personal and it's not uncommon. Lenders are being very cautious about which loans they approve and are watchful for errors by all involved. Appraisals are an "opinion" of value and not a scientific certainty. Two different appraisers may come to two different opinions and often do.
It's likely that there is something about the first appraisal that they were uncomfortable with and want a second opinion.
(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.
Hopefully a licensed appraiser will chime in with other explanations. Sometimes the reason for a second appraisal are not disclosed to the buyer at all.