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It appears that the Speck6496KeySchedule as shown in the implementation guide tries to save a round key at an index that is out of bounds. This version of the Speck cipher has 26 rounds, which requires equally many round keys. The key schedules last assignment rk[i]=A; is for index 26, the 27th round key.
This instruction shouldn't be there, all required round keys have already been generated.

Version from the "SIMON and SPECK Implementation Guide" [0]:

void Speck6496KeySchedule(u32 K[],u32 rk[])
{
    u32 i,C=K[2],B=K[1],A=K[0];
    for(i=0;i<26;){
        rk[i]=A; ER32(B,A,i++);
        rk[i]=A; ER32(C,A,i++);
    }
    rk[i]=A;
}

Fixed version:

void Speck6496KeySchedule(u32 K[],u32 rk[])
{
    u32 i,C=K[2],B=K[1],A=K[0];
    for(i=0;i<26;){
        rk[i]=A; ER32(B,A,i++);
        rk[i]=A; ER32(C,A,i++);
    }
}

[0] R. Beaulieu, D. Shors, J. Smith, S. Treatman-Clark, B. Weeks and L. Wingers,
"SIMON and SPECK Implementation Guide", NSA Cybersecurity, June 26, 2018. [Online].
Available: https://nsacyber.github.io/simon-speck/implementations/ImplementationGuide1.1.pdf