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[[meta:Help:Template#Mix of named and unnamed parameters]] explains this problem. The last sentence is particularly relevant: "the direct assignment of the value '1' to parameter 3 is later overwritten by the third unnamed parameter."

For instance, if you write {{example template|3=A|B|1=C|D|E}}, and the template consists simply of {{{1}}}-{{{2}}}-{{{3}}}, the result would be C-D-E rather than the more logical C-B-A (where the "first" unnamed parameter, B, takes the place of the first unassigned numbered parameter) or C-D-A (where simply explicitly numbered parameters take precedence over the implicit numbering).

I think the first alternative, C-B-A, makes most sense, but either approach would be better than the current behavior.