Can a urinary tract infection and bacteria infection give you a missed period or make you pregnancy test negative? I have both my period is 3days late

Both unlikely. You may repeat the pregnancy test in 3-4 days,if you do not get a period by then, use first morning urine and follow the instructions carefully. See this site for information on this topic. http://www.nichd.nih.gov/health/topics/menstruation/conditioninfo/Pages/causes.aspx.
No, neither. No infection will affect your menstrual cycle, nor the results of pregnancy test. Based on the info you gave you are late but not pregnant. The most common reason (besides pregnant) is a late or skipped ovulation; it's common. You can wait up to one month for the next period; if you do, it might be good to repeat the pregnancy test in a few days to be sure. Good wishes.
Possibly. A urine test may be negative if is done too early, dilute urine is used or interfering substances (proteins or infection). If you are concerned then request a blood test.

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