Why is there so much hate/dislike/prejudice/discrimination/intolerance/... among groups in the world. Even religious groups which espouse a "Love your Neighbor" philosophy/theology.
This is expressed in a variety of ways from exclusion, separation, ostracization, segregation, prejudice, bias, bigotry, racism. All the way up to violence, rebellion, wars and genocide.

Inter-racial degradation -:

• 1619 - : African American slavery and discrimination in the US
  See Slavery in America - Black History - HISTORY.com
• 1850: The English thought that the Irish and Scotts were inferior.
• 1935: Nazi Germany - Superiority of Nordic or Aryan races.

• Christian - Islam: Crusades, Al Qaeda (al-Qa'ida), Islamic State in Iraq and Syria (ISIS)
• Jewish - Muslim: Arab-Israeli wars
• Suni - Shia: Two Islam sects
  See Suni - Shi'a
• Protestants - Catholics: Reformation, N. Ireland
• Communism vs Religion: Russia, China, ...

See also Dictators and Genocide
Terrorism

Empire expansion:
Of course there have been battles for expanding empires for millennia. The Sumerians (3,000 BC), Egyptians (3,000 BC), Trojan (1,190 BC), Israel vs the Philistines (1,000 BC), Babylonians (1,100 BC), Persians (500 BC), ... Arabs (600-1,000), Crusades (1,100-1,200), Ottoman (1,453-1,566), British, Spanish, ...
See Wars, Battles, Insurgencies, Rebels and Empires

This question has been troubling me for some time now. I've thought about it a lot, but haven't even scratched the surface in looking for answers.

It came to the forefront for me in 2015 when the Presbyterian church I've been a member of for 28 years voted to leave the PCUSA (The largest national Presbyterian denomination with 2 million members) for a new more conservative church, A Covenant Order of Evangelical Presbyterians (ECO) with about 85,000 members.
The church where grew up and four generations of my family were founders and active, the First Presbyterian Church of Roseville (CA) left PCUSA for the Evangelical PC in 2007.
See Presbyterian Church USA Issues

A couple of theories I've come up with with no hard evidence to back them are:
The Tribal Gene
Self-Esteem by putting down others.

Books:
Disunity in Christ: Uncovering the Hidden Forces that Keep Us Apart , 2013 Christena Cleveland

Links:
Intergroup Relations, Messick and Mackie, 1989, UC Santa Barbara
Intergroup Relationships - Introduction to Sociology - OpenStax CNX
Os Guinness: Getting Along, Despite Differences
Tollerance in religion here
Presbyterian Church USA Issues