Look in the Fitter Report's Global usage to see if they're separate clocks. In TimeQuest you can look at them with:
report_timing -full_path -to_clock {clk|ref_160_40|altpll_component|auto_generated|pll 1|clk[0]} -panel_name "clk0"
report_timing -full_path -to_clock {clk|ref_160_40|altpll_component|auto_generated|pll 1|clk[0]~1} -panel_name "clk0~1"
You can also do -from_clock -to_clock to analyze paths going between them. Naturally, I can't tell what's going on from the original post, but it does look like it's being split for some reason. Generally not good, but hard to tell.
(I have seen cases where this is done and I applied a Global Signal assignment in Assignment Editor and it helped fit it, but not always. There may be a specific reason this is being done.)