Mood for touch, kiss doesnt indicate mood for sex. Also if this has happened only once, there is No cause for worry. A person cant start having erection at an instant's notice.
Sex needs time to kindle. Unfortunately with today's instant gratification trend in society, people have unrealistic expectation of self and partner.
You said your boner "doesnt last long" and it " doesn,t get fully erect" when your partner tries to handle it and rub it.
This suggests you were not aroused.
Clandestine sex carries a baggage of problems and this may reflect in non erect penis, early ejaculation, sex not being pleasurable, and other issues.
This is NORMAL. It doesnt mean you have problems. Its a mere dys function and not a disease.
Next Steps
try to build a sexy mood before attempting sex, communicating with each other by verbal or electronic media like sms, whatsapp etc. Then when together, do lots of non naked hugging, petting. This will build the mood gradually. If you feel you are erect, only then try to have any handling of the penis. Your partner must be made aware that lack of excitement in a man is NOT suggestive of his "lack of interest in her"