Contraindications are situations in which a procedure may be harmful of ineffective, here we're compiling a list of such things which may interact in a negative way with HRT.
Feminizing HRT Risk Factors
Deep vein thrombosis (DVT) was largely regarded as a risk heightened by hormone replacement therapy based on studies exploring the effects of estrogen and estrogen-progestin on post-menopausal women. This data has proven beneficial in suggesting transdermal HRT decreases the risk in contrast to oral method of administration and that age of an individual also increases DVT in conjunction with estrogen 
Thanks to a recent study specific to incidence of DVT in transgender women recieving estrogen orally, further evidence has been provided to suggest that the risk factor was largely an overstatement- a frequently cited decades old article  was prior used to prove the DVT risk, but it focused entirely on ethinyl estradiol in contrast to the more commonly prescribed 17b-estradiol. The results of the study stated that using a sample group of 676 transgender women from 2008-2016 with an average time on HRT being 2 years, only one individual (0.015%) had sustained DVT.
- nicotine use can increase risk of deep vein thrombosis which is already a significant risk with consuming exogenous estrogen, to the point some doctors will insist on the patient quitting prior to prescribing HRT. It is also an antagonist at estrogen receptor beta and has thus been implicated in causing detrimental effects in brains. 
- caffiene in excessive quantities can accelerate estrogen metabolism by upregulating the enzyme responsible for metabolizing both caffiene and 17b-estradiol, and thus lead to depletion of administered estrogen faster than would otherwise occur. 
- Hormone replacement therapy and venous thromboembolism
- Incidence of Venous Thromboembolism in Transgender Women Receiving Oral Estradiol (2016)
- Mortality and morbidity in transsexual subjects treated with cross-sex hormones
- Nicotine Addiction Causes Unique Detrimental Effects on Women’s Brains | https://www.ncbi.nlm.nih.gov/pubmed/21491296
- Relationship Between Caffeine Intake and Plasma Sex Hormone Concentrations in Premenopausal and Postmenopausal Women | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2764240/