To expand on the excellent answer by haci:
BLAST reports (a) the summary of alignments and (b) individual alignments, see below. Note that your link to the results expired (as NCBI BLAST results links tend to do). It is considered best practice to post the text version of the relevant portion of the results in the question itself.
The summary provides an overview of all the query sequence individual hits in the subject sequence. Because the individual hits (alignments, or ranges) together cover 100% of the query and each of these has the max identity = 100%, that is what it reports in the summary. It is not very intuitive for many users.
You should always look at the individual hits in detail. The above 100% coverage in the summary consists of ranges 1 and 14, shown below. The top hit (range 1) covers only 17 out of 21 nt with 100% identity, and this is the most relevant information from BLAST. The other hit (range 14) covers 10 out of 21 nt with 100% identity. This is the cause of the discrepancy.
These 2 alignments are not close together in the subject sequence. Depending on your goal, choose one or more of the individual alignments and consider alignment length and % identity of those hits individually, rather than summarized together as in the BLAST report summary. For most applications, the top hit (range 1) would be the most relevant alignment.
Subject:Neisseria meningitidis strain M22814 chromosome, complete genome ID: CP031332.1(nucleic acid) Length: 2190201
Query #1: seq1 Query ID: lcl|Query_56011 Length: 21
Sequences producing significant alignments:
Max Total Query E Per.
Description Score Score cover Value Ident Accession
Neisseria meningitidis strain M22814 chromosome, complete genome 34.2 57729 100% 0.001 100.00 CP031332.1
>Neisseria meningitidis strain M22814 chromosome, complete genome
Sequence ID: CP031332.1 Length: 2190201
Range 1: 2074883 to 2074899
Score:34.2 bits(17), Expect:0.001,
Identities:17/17(100%), Gaps:0/17(0%), Strand: Plus/Plus
Query 1 CAATTGCGAAGCCACAT 17
Sbjct 2074883 CAATTGCGAAGCCACAT 2074899
Range 14: 354292 to 354301
Score:20.3 bits(10), Expect:15,
Identities:10/10(100%), Gaps:0/10(0%), Strand: Plus/Minus
Query 12 CCACATTATT 21
Sbjct 354301 CCACATTATT 354292