"Theology of the Body," originally called "Catechesis on Human Love," is based on the philosophies of phenomenology and personalism (basically humanism), contradicting Thomistic teaching on several points:
Against Summa Theologica II-II q. 151 a. 1 co., which says
Chastity takes its name from the fact that reason "chastises" concupiscence […] the essence of human virtue consists in being something moderated by reason, John Paul II thought St. Thomas incorrectly classified chastity as a virtue of temperance (Petri, O.P. p. 114n118). Cf. ibid. p. 166n12, which cites ToB no. 54: John Paul II "disagrees with Aquinas's conception that purity 'consists above all in holding back the impulses of sense-desire.' See also ibid., no. 130."
Against Summa Theologica III q. 64 a. 1 co. (which pairs the sacrament of "Matrimony," "a remedy against concupiscence in the individual", "to Temperance, being ordained against concupiscence"), John Paul II thinks the remedium concupiscentiæ end of marriage is outdated. Cf. ToB no. 84 §8:
Does the Apostle in 1 Corinthians see marriage only from the point of view of a "remedium concupiscentiae [remedy for concupiscence]," as one used to say in traditional theological language?
Against Summa II-II q. 152 a. 4 co. (cf. Trent sess. 24 can. 10), John Paul II thinks the state of virginity or celibacy is not superior to that of marriage (ToB no. 78):
Christ’s words reported in Matthew 19:11–12 (like Paul’s words in 1 Cor 7) give us no reason for holding either the "inferiority" of marriage or the "superiority" of virginity or celibacy on the grounds that by their very nature the latter consists in abstaining from conjugal "union in the body."cf. Gustavo Daniel Corbi, “Jovinian '82: The Resurrection of a Heresy,” trans. J. S. Daly, ICTION, Buenos Aires, 1982., whose appendix analyzes ToB no. 78.
John Paul II himself even noted ToB's limitations (Memory & Identity p. 12):
If we wish to speak rationally about good and evil, we have to return to St. Thomas Aquinas, that is, to the philosophy of being. With the phenomenological method, for example, we can study experiences of morality, religion, or simply what it is to be human, and draw from them a significant enrichment of our knowledge. Yet we must not forget that all these analyses implicitly presuppose the reality of the Absolute Being and also the reality of being human, that is, being a creature. If we do not set out from such 'realist' presuppositions, we end up in a vacuum.
cited at the end of Petri, O.P.'s talk Aquinas & the Theology of the Body; cf. his book of the same title