User blog comment:Skyblade743/Every Unsolved Question in Sonic./@comment-32712012-20171227115908

Sonic '06 sometimes acts as though traveling to the past can change the present (e.g. Sonic goes back in time to prevent Elise's death), while at other times, it acts as though anything that you do when traveling to the past happened all along (e.g. Mephiles is released from the Scepter of Darkness, indicating that he knows Shadow; then Shadow goes to the past and seals Mephiles in the Scepter of Darkness, only then realizing why Mephiles knows him).

TL:DR; Sonic '06 has two conflicting varieties of time travel.