Cross-dressing was considered blasphemous.
From the transcript of her trial:
It is sufficiently notorious and well-known that for some time past a woman calling herself Jeanne the Pucelle, leaving off the dress and clothing of the feminine sex, a thing contrary to divine law and abominable before God, and forbidden by all laws, wore clothing and armour such as is worn by men; [...]
Asked whether her saying that she would take a woman's dress if they would let her go, was pleasing to God, she answered that if they let her go in a woman's dress, she would at once put on man's dress and do as Our Lord commanded her. She has said this before. And she would not for anything take the oath that she would not take up arms or wear male dress to do Our Lord's will. [...]
As to the Thirteenth, accusing her of blasphemy [in saying that it was at God's command that she put on male clothing, 'violating canon law, to the scandal of her sex and womanly modesty, and to the perversion of all decent behaviour.']: She answered: I have blasphemed neither God nor His saints. And after it was explained to her that according to canon law and the Holy Scriptures the taking by women of man's dress and the taking by men of woman's dress is an abomination before God, they asked her whether she had taken the said dress by God's command, she said: You have been answered as to this before: and if you wish me to answer again, then grant me a delay, and I will answer you. Being asked whether she would take a woman's dress so that she might receive her Saviour at Easter, she answered that she would not leave off her [man's] dress either to receive her Saviour or for any other reason. She added that to receive her Saviour neither man's nor woman's dress made any difference; and It ought not to be refused her on account of this dress. [...]
You have said that, by God's command, you have continually worn man's dress, wearing the short robe, doublet, and hose attached by points; that you have also worn your hair short, cut en rond above your ears, with nothing left that could show you to be a woman; and that on many occasions you received the Body of our Lord dressed in this fashion, although you have been frequently admonished to leave it off, which you have refused to do, saying that you would rather die than leave it off, save by God's command. And you said further that if you were still so dressed and with the king and those of his party, it would be one of the greatest blessings for the kingdom of France; and you have said that not for anything would you take an oath not to wear this dress or carry arms; and concerning all these matters you have said that you did well, and obediently to God's command. As for these points, the clerks say that you blaspheme God in His sacraments; that you transgress divine law, the Holy Scriptures and the canon law; you hold the Faith doubtfully and wrongly; you boast vainly; you are suspect of idolatry; and you condemn yourself in being unwilling to wear the customary clothing of your sex, and following the custom of the Gentiles and the heathen. [...]
From Clothes Make the Man: Female Crossdressing in Medieval Europe:
Regardless of the cause of the return to male dress, transvestism remains a primary reason for condemnation. During the rehabilitation hearings, witnesses to the event in Rouen were asked why she was charged with being a relapsed heretic after she had clearly stated her willingness to submit herself to the pope. Everyone of them cited the reversion to male dress as the reason. Pierre Cusquel stated this succinctly: “Populus dicebat quod nulla erat alia causa condemnationis suae, nisi resumptio habitus virilis.” [The people said there was no other cause for her condemnation, except the resumption of masculine clothing.]
Even among the supporters of Jeanne’s rehabilitation one senses an uneasiness toward her cross dressing. For the most part, they overlooked her own explanation for transvestism when they defended it as a protective device or blamed her enemies for forcing her to put on men’s clothes after the abjuration. They shied away from extolling her transvestism but offered various excuses to legitimate it within the Christian tradition. For example, the rehabilitation proceedings include a defense for receiving the sacraments in male dress grounded in hagiographic precedence:
[...] [It ought not to be judged heretical if she received the sacrament in this habit (male dress), since it had been taken up out of necessity for her duty and office, and it was worn for a good cause. Just as no one will fault blessed Marina, who was accused of a crime, if, continually in men’s clothes, she dwelt incognito in the monastery of monks, communicating in the sacraments with the monks. Similarly, concerning blessed Eugenia, who lived for a very long time and very chastely in men’s clothes.]
Jeanne apparently never made such excuses during her trial, although they were attributed to her by later authors. In fact, she failed to use any of her supporters’ defenses for transvestism at her trial. She neglected to cite examples of biblical heroines and transvestite saints, although it is likely that she had heard of such precedents either from French encomiasts in their tributes to her or from her own religious upbringing. Instead, she persisted in the unprovable claim that God was the source of her transvestism. Perhaps she ignored biblical and hagiographic precedents because they were not her models. Unlike Jeanne, Judith and Esther used womanly charms to succeed, and although she also has been compared with female monks, her goal was not the imitation of meek men. The transvestite saints’ lives of self-effacement in the cloister had little in common with Jeanne’s military career. Even Camilla, Penthesilea, and Semiramis, the classical female warriors, whom Jeanne, with her limited education, may not even have known, offered no analogy to her divinely ordained transvestism. Jeanne was obviously not concerned with precedents; she emphasized the importance of her male dress without apology because it distinguished her, served as a source of strength, and, she maintained, represented God’s will.
I've made my case for Jeanne d'Arc as a part of both trans and women's histories in this post, but essentially the point is not that I think Joan identified as not-a-woman, it is that she crossdressed for the sake of crossdressing and found it personally meaningful to her, and her gender deviance was used as justification to kill her. It was the gender deviance that was a part of the heresy, particularly because she claimed it was commanded by God. She suffered as a result of transphobia and misogyny, even if that was not the only thing at play.
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