DONE!!!!: 25/25 answered Thanks Jafe for a really good puzzle.
1: Concealed Yugoslav introduces military cemetery (6)
SLAVIN (Bratislava, Slovakia) Concealed in YugoSLAV INtroduces.
2: Buddhist temple is top three watching photos
WAT PHO (Bangkok) WATching PHOtos (top three)
3: Central square hides koala to observatory (3-3)
ALA TOO Square in Bishkek, Kyrgyzstan koala to observatory.
4: Thriller writer John adds three lines to palace (7)
GRESHAM (Budapest) GRISHAM + 3 lines converts I to E (Made possible after addition of JOHN to clue -- I was playing around with KING + III or ILI etc but it lead nowhere)
5: Extra work removed and added in Bogota national museum (7)
BOGANDA (Bangui, C.A.R.) BOGATA - OT + AND (inside) Very nice clue!
6: Male cat in capsicum's sonorants leads to iconic building (7)
A(TOM)IUM (Brussels) -- Sonorants are voiced letters AIUM from Capiscum.
7: Matrix creator held by philosopher loses a presidential palace (8)
PLANALTO (Brasilia) PLA(NAL)TO LANA (Wachowski) Inverted, loses A
8: Muppet has tea after initially seeking a new neighbourhood (3 5)
SAN TELMO (Neighbourhood in B.A. Argentina) ELMO (muppet) has T (tea) after Seeking A New (initially)
9: Marina equals ship's tilt and lifetime thus far (9)
CAREEN+AGE Marina in Bridgetown Barbados.
10: Improperly unmask duo to museum (4 5)
Musée de la femme MUSO KUNDA (BAMAKO MALI) Anagram of Unmask Duo
11: Rename, sort, rearrange Andean hilltop (10)
MONSERRATE (Bogota, Colombia) Anagram of "Rename Sort"
12: Canonical uncorked Spanish wine has second Orthodox church (5 4)
SAINT SAVA (BELGRADE, Serbia) Canonical ~~ SAINT, Spanish Wine = CAVA, Uncorked (remove top) = AVA has S for second. IMO, this is the weakest clue in an otherwise excellent puzzle
13: Place of worship with unique queue after Def following face part (4 6)
CHIN MOSQUE (Baku, Azerbaijan) CHIN + MOS (Rapper Mos Def) + QUE(ue) I'm not entirely sure how to get the QUE out of UNIQUE QUEUE, but it could be QUE as a string (queue) of letters from UNIQUE. I'm reasonably certain of the answer.
14: Old court crook has hot drink with revolutionary (5 5)
CURTEA VECHE (Bucharest) (Old Princely Court) -- CURVE (crook, as in bend) with TEA + CHE. I'm pretty certain on this one, even though the count doesn't match.
15: Natural formation doves are awesome (7 4)
Pigeons' Rock (Beirut) (this one should be obvious to parse)
16: Endless Nigerian people follow German physicist to former residence (12)
EINSTEINHAUS (Bern) HAUSa (Nigerian people, endless) following EINSTEIN for Albert Einstein's former residence
16 Alt: A stone house in German fashion (12)
EINSTEINHAUS A STONE HOUSE in German
17: Camus alongside Swedish border islet leads to place for shopping (6 6)
ALBERT MARKET (Banjul, The Gambia) ALBERT Camus + MÄRKET island shared by Finland and Sweden
18: Mbabane wrote twisted skyscraper (7 5)
Nabemba Tower (Brazzaville, Congo) Anagram (twisted) of Mbabane Wrote
19: Imperial palace to ban mass per volume, or so I've heard (9 4)
FORBIDDEN CITY (Beijing, China) FORBID + DEN CITY (Density homophone)
20: Limbs of triumph is sword monument (5 2 7)
HANDS OF VICTORY (Baghdad, Iraq)
21: Fortress to perversely maraud following Brazilian city
Fortaleza d'Amura (Bissau, Guinea-Bissau) Fortaleza (Brazilian City) + anagram of MARAUD
22: Bay Area city's commemorative monument is clock tower (8 8)
BERKELEY MEMORIAL (Basseterre, St Kitts & Nevis) Obvious parsing. Was red-herringed to the OAKLAND MEMORIAL in Mississippi, and the clue change didn't really help much, but the confirmation on the count did.
23: Former border crossing to verify location C (10, 7)
CHECKPOINT CHARLIE (Berlin, Germany) CHECK + POINT + CHARLIE (Phonetic C)
24: Mosque dad unifies moral AI in disguise (4 3 10)
Omar Ali Saifuddien ( Bandar Seri Begawan, Brunei) anagram of "dad unifies moral AI"
25: National park is somber gap after German tanks having car model (2. 6'1 4 4)
ST. HERMAN"S BLUE HOLE (Belmopan, Belize) ??? S(T)HERMANS (Tanks with Model T) + BLUE (Somber) +HOLE (gap)
All locations are in or near a Capital city beginning with B -- Thanks M OEHM for the hint. Made the rest possible.
This was a really good puzzle. Anagram indicators were clear. Every answer had a degree of certainty that made me know I was right when I finally untangled the devious web that Jafe had created. There was some nice misdirection, and some really clever wordplay. I'm not all that happy with 12, not fully accepting that CANONICAL = SAINT. Close, but not really. FWIW, I got 2 without research. Beijing and Berlin. Everything else was solved using Wikipedia "List of ..." and a few (2, 8, 13) were solved by wordplay alone then a google check to see if that thing exists. A couple of times, google's "Did you mean?" yielded the critical hint.