Occasionally a small injury to a prostatic vein does stain the prostatic Fluid and thus the ejaculate brown. It may not be of any significance but recurrence demands an urological opinion.
Semen appearance and texture can change naturally over the course of months, days, or even from one ejaculation to another, due to a variety of factors including diet.
Semen from a mature male is usually a milky or pearly-white color. It is not uncommon to see a yellowish tint to the semen if you've abstained from ejaculation for a while. Semen colored with red streaks may signify blood. If you occasionally see a bit of blood it's not necessarily a cause for alarm, but if you see a lot of it, or if it persists, the condition should be brought to the attention of your physician. The same goes any other drastic color changes, which may indicate infection.
A lot of factors go into the appearance and consistency of semen, including diet, ejaculation frequency, etc., so changing any of these can alter the way your semen looks. Also, it's easy to think that semen is simply sperm cells in Water, but it's a much more complex substance than that. So it may have been the absence or presence of something other than actual sperm cells — such as sugars or Proteins — that caused your semen to look different before.
A nocturnal ejaculation may have more prostatic fluid in it (which is whiter and thicker), while a daytime ejaculation may have more sperm and fluid from the seminal vesicles, which tends to be more clear and less viscous.
If your semen is stained with a red or brown colored fluid it may well be blood. Sometimes a small blood vessel may burst when you ejaculate. Within a day or two the semen should return to its normal state so there should be no need to worry. If it continues then you should see your doctor. Blood in semen may be present for many different reasons, such as infection, trauma and sometimes, but rarely, cancer. Normal semen may have an off-white or yellowy hint to the color. Where semen is uncharacteristically yellow in color it is a sign of infection, treatment is simple with antibiotics.