I have explained in Revising the classification of Indo-European languages that Latin and Greek are probably hybrid languages with two major components: one Indo-European, and the other from an unknown West Asian language (probably long extinct). There may also be older Neolithic loanwords.
It is evidently hard to identify words from an unknown extinct language, so the best way to proceed to to sieve the words that cannot be ascertain as Indo-European. This includes all the roots of unknown or uncertain origin.
I will start by listing Latin words with their Italian and French derivatives, and show the lack of resemble to the Proto-Indo-European root.
Latin (French, Italian) >< PIE root
- manducare (manger, mangiare) >< *ed-
EDIT : here are more words
- amygdala/amandula (amande, mandorla), from Greek amygdalos but not found in other IE languages
- autumnus (automne, autunno), of unknown origin, possibly from Etruscan.
- bestia (bête, bestia)
- coda (queue, coda), unrelated to the PIE *puk(eha) or *wolos
- elementem (element, elemento)
- cylindrus (cylindre, cilindro) only related to Greek kylindros
- famulus : Latin word for servant from which "family" is derived. Unrelated to the PIE roots *genhes or *wik
- farcire (farcire, farcire)
- finis (fin, fine), unrelated to the PIE root *termn-
- honorem (honeur, onore), not found in other IE languages
- largus (large, largo), unrelated to the PIE *megha or *mehro
- male/malus (mal, male), not related to PIE *ghalh(x)ros nor *hedwol
- metallum (métal, metallo), from Greek metallon, but differs from PIE word *h(a)eyes
- miser (misère, misera), no similarity with other IE languages
- (s)mittere : Latin word meaning "to send" used as a root for many words (transmit, emit, permit, etc.). No IE cognate.
- nigrum (noir, nero), unrelated to the PIE *k(w)rsnos, *mel-n or *keir
- oceanus (ocean, oceano), from Greek oceanos, but no cognates in other IE
- ochra (ocre, ocra), from Greek ochra, but no cognates in other IE
- phrasis (phrase, frase), from Greek phrasis (speech, way of speaking), but doesn't cognate with any IE word
- populus (peuple, popolo), no cognate in other IE languages. Possibly from Etruscan.
- purpura (pourpre, purpureo), from Greek porphyra which is of Semitic origin
- radius (rayon, raggio/radio)
- sanguis (sang, sangue), unrelated to the PIE *bhlo-to
- silens (silence, silenzio), doesn't appear to be IE
- sphæra (sphère, sfera) from Greek sphaira (globe, ball), of unknown origin.
- totus/totalis (total, totale), no IE cognate
- verdis (vert, verde), unrelated to the PIE *ker-, *kr-wos or *modheros, or to the PIE base *ghre- ("grow", from which the Germanic green derives)
- volare (voler, volare), unrelated to the PIE *dih- or *pet-
- auto- : prefix meaning "self", doesn't cognate in other IE languages
- mythos : "speech, thought, story, myth," of unknown origin.
- elektron : Greek word for amber, no cognate in IE
- xanthos : Greek word for yellow, no cognate in IE
- The Greek for "thousand" (kilo or khilias) as well as the Latin one (mille) are unrelated to the PIE root *tuh(a)s-kmtyos found in all Germanic and Balto-Slavic languages.