A repair kit could have included a slightly different wire circlip and you re-used the original "square wire" one that came out.
Or a PO may have left one inside the old rubber boot and it fell out.
There's a wavy spring washer under the plastic valve spacer at the back of the M/C, but I don't think you would describe that as a wire clip.
Hard to know for sure with these odd ball things. Anyhow, only one retaining circlip is needed.
Regards,
Viv.