Psalm 139:7-10 " Whither shall I go from thy spirit? or whither shall I flee from thy presence? If I ascend up into heaven, thou art there: if I make my bed in hell, behold, thou art there. If I take the wings of the morning, and dwell in the uttermost parts of the sea; Even there shall thy hand lead me, and thy right hand shall hold me. "
Genesis 11:5 "And the LORD came down to see the city and the tower, which the children of men builded."
Genesis 18:20-21 "And the LORD said, Because the cry of Sodom and Gomorrah is great, and because their sin is very grievous; I will go down now, and see whether they have done altogether according to the cry of it, which is come unto me; and if not, I will know."
The passages from Genesis about God "coming down to see" seem to indicate that God surely is not everywhere present, or else why would He have "to come down" to some place? The passage from Psalm 139 on the other hand clearly indicates that God is present in even most contrasting places (heaven and hell; east and west).
Once again in these cases, we must understand that in certain places in Scripture God is attributed human characteristics, this is done by way of the figure of speech "condescensio". God, as a spirit, who "inhabits eternity" (cp. Isaiah 57:15) is indeed everywhere present and He need not literally go some place or come down to some place to actually be present there. Such references about the LORD going to Babylon to take a look at the tower which the folks there had built, or about the LORD going to Sodom to see if it was true what He had heard about that place, are the use of this figure of speech. Something is expressed in human terms for emphasis and perhaps a better understanding on the reader's part. God is not "coming" to these places in a phyiscal sense, rather He is turning His attention there and is going to deal with that particular situation.
When we understand the figure of speech involved in the expressions used, and when we observe the contexts of each passage, we can easily see that there is not discrepancy nor contradiction whatever between these sections of Scripture.