How does blastn sort output? I used blastn to search one a genome database for the sequences in a file. 

blastn -out output.txt -outfmt 6 -query sequence_list -db genome_database -perc_identity 100


These sequences are all from one contig of the genome so the output was all hits in one contig. I then appended more sequences to the sequence file and used blastn again. However the weird thing is the output did not start with the same hits as the last blast. I expected if blastn iterated through sequences in a query file that it would output the original sequences first then go through the appended sequences. Since this was not the case, how does blast order its output?

I also checked if it was sorted by which contig the hit was in and this is not the case.
BLASTN should definitely report alignments in the order that the query sequences were provided.

Based on your description and my personal experience, I think the most likely explanation is some kind of mix up. It happens to all of us, especially when we're in a rush to get an answer, but even sometimes when we're being careful and disciplined.

If you can go back and recreate the result, I would be very interested to see the two pairs of input and output files. If not, I wouldn't spend too much more time worrying about it. :-)

UPDATE Alignments are reported in the order that the query sequences are provided, even in tabular mode. The order of each query's hits is sorted by bitscore or e-value, but that is a secondary sorting. I've included an example below that has two queries, seq1 and seq2 with -outfmt 6.

seq1    scaffold2       100.000 280     0       0       1       280     11131   11410   7.73e-146       518
seq1    scaffold294     88.693  283     25      4       1       279     12160   12439   6.46e-92        339
seq1    scaffold1525    85.315  286     29      9       1       277     27142   26861   3.07e-75        283
seq1    scaffold1874    83.505  291     32      10      1       280     8558    8273    1.86e-67        257
seq1    scaffold147     82.653  294     34      9       1       279     10797   10506   1.45e-63        244
seq1    scaffold2478    82.374  278     38      8       11      280     7622    7896    1.13e-59        231
seq1    scaffold3405    87.940  199     17      5       1       196     14390   14584   1.46e-58        228
seq1    scaffold395     83.060  183     23      4       106     280     12021   11839   5.40e-38        159
seq1    scaffold2853    85.965  114     13      3       1       113     20864   20753   9.16e-26        119
seq2    scaffold9       100.000 140     0       0       1       140     1121    1260    2.34e-68        259
seq2    scaffold2950    90.909  110     6       3       1       106     110     1       6.84e-34        145
seq2    scaffold3416    95.385  65      3       0       1       65      11882   11818   1.16e-21        104
seq2    scaffold3103    95.385  65      3       0       1       65      9736    9672    1.16e-21        104
seq2    scaffold5297    88.608  79      7       1       64      140     150     228     6.99e-19        95.3