The phonological system of proto-Indo-European (and of any other proto-language without written records) is reconstructed via the comparative method, which inevitably leaves some questions open.
One such open question is the stops' manner of articulation problem. There are currently the two competing viewpoints concerning this problem - the traditional theory (which claims that stops were pronounced as voiced, voiceless, or murmorred) and the glottalic theory (which proposes that stops were pronounced in an ejective, plain, or (breathy) voiced manner). It should be mentioned, though, that in all other aspects the two theories agree i.e. given the available data, pIE had exactly 3 distinct rows of stops; there were 5 places of articulation - labial, dental, palatal, velar, labio-velar; roots couldn't contain a sequence of traditional "plain voiced" stops or a combination of a traditional "voiceless" and a "breathy voiced" stop...
I am fully aware that as of today nobody can give an unambiguous answer to the manner-of-articulation dilemma, however, I was wondering how confident we can be regarding the remaining assumptions? In particular, what is the proof the pIE didn't have retroflex stops? Or that it lacked affricates? In general, can we be sure that there are no major gaps in the pIE phonological system?
Remark: One particular peculiarity of pIE that incited me to ask the above question is that it had 3 varieties of velar stops (palatal, plain, and labio-velar), while the coronal and the labial stops had just one. If, for example, there were retroflex coronal stops, then the picture would have been more "balanced".