Cool on ice. Concentration of vector DNA should normally be Calculation to obtain the best vector and insert concentration is normally not required. If the background is low, there is no need for screening of the transformed cells for vector with ligated insert. Only use phosphatase when strictly necessary.
Fewer steps means less problem.
Also use the best grade agarose or low m.p. agarose for the gel. DNA should always be gel-purified before ligation. Some enzymes have been suggested to be able to stick to the ends of DNA thereby affecting ligation. There is uncertainty if this is the case, or if it is a problem of enzyme carrying over during purification. Taq polymerase, for example, may not be completely removed during purification and can fill in the digested end of DNA and thereby preventing ligation.