Interesting observation. ALL my references have the complaint sense second, but I just looked at the Tanaka/Tatoeba sentences, and I see that there are 64 which use 文句, of which 3 use the "phrase" sense and 61 the "complaint" sense. I agree there's grounds for striking out here.
(Of course I now have to edit those 64 sentences.... Fortunately I can do some global changes.)

daijs prog 新和英中辞典

probably most commonly used to mean "complaint", especially 
when used by itself
(though all three refs does keep the same order as the 
original entry)

@@ -18,1 +18,3 @@
-<gloss>phrase</gloss>
+<gloss>complaint</gloss>
+<gloss>grumbling</gloss>
+<gloss>objection</gloss>
@@ -22,1 +24,3 @@
-<gloss>complaint</gloss>
+<gloss>phrase</gloss>
+<gloss>words</gloss>
+<gloss>expression</gloss>