Git over HTTP(S) stopped working (HTTP Basic: Access denied)

Summary

After some of the latest updates (13.12.3) Git over HTTP(S) stopped working on our private Gitlab CE instance.

What is the current bug behavior?

user@server:$ git clone https://gitlab.../issues.git
Cloning into 'issues'...
Username for 'https://gitlab...': username
Password for 'https://username@gitlab...':
remote: HTTP Basic: Access denied
fatal: Authentication failed for 'https://gitlab.../username/issues.git/'

What is the expected correct behavior?

user@server:$ git clone https://github.com/ImDwivedi1/Git-Example.git
Cloning into 'Git-Example'...
remote: Enumerating objects: 31, done.
remote: Counting objects: 100% (31/31), done.
remote: Compressing objects: 100% (26/26), done.
remote: Total 31 (delta 7), reused 6 (delta 1), pack-reused 0
Unpacking objects: 100% (31/31), done.

Relevant logs and/or screenshots

Output of checks

Results of GitLab environment info

Expand for output related to GitLab environment info

System information
System:
Current User:   git
Using RVM:      no
Ruby Version:   2.7.2p137
Gem Version:    3.1.4
Bundler Version:2.1.4
Rake Version:   13.0.3
Redis Version:  6.0.12
Git Version:    2.31.1
Sidekiq Version:5.2.9
Go Version:     unknown

GitLab information
Version:        13.12.3
Revision:       757327a59bc
Directory:      /opt/gitlab/embedded/service/gitlab-rails
DB Adapter:     PostgreSQL
DB Version:     12.6
URL:            https://gitlab...
HTTP Clone URL: https://gitlab.../some-group/some-project.git
SSH Clone URL:  git@gitlab...:some-group/some-project.git
Using LDAP:     yes
Using Omniauth: yes
Omniauth Providers:

GitLab Shell
Version:        13.18.0
Repository storage paths:
- default:      /var/opt/gitlab/git-data/repositories
GitLab Shell path:              /opt/gitlab/embedded/service/gitlab-shell
Git:            /opt/gitlab/embedded/bin/git

Results of GitLab application Check

Expand for output related to the GitLab application check

Checking GitLab subtasks ...
Checking GitLab Shell ...
GitLab Shell: ... GitLab Shell version >= 13.18.0 ? ... OK (13.18.0)
Running /opt/gitlab/embedded/service/gitlab-shell/bin/check
Internal API available: OK
Redis available via internal API: OK
gitlab-shell self-check successful
Checking GitLab Shell ... Finished
Checking Gitaly ...
Gitaly: ... default ... OK
Checking Gitaly ... Finished
Checking Sidekiq ...
Sidekiq: ... Running? ... yes
Number of Sidekiq processes (cluster/worker) ... 1/1
Checking Sidekiq ... Finished
Checking Incoming Email ...
Incoming Email: ... Reply by email is disabled in config/gitlab.yml
Checking Incoming Email ... Finished
Checking LDAP ...
LDAP: ... Server: ldapmain
LDAP authentication... Success
LDAP users with access to your GitLab server (only showing the first 100 results)
User output sanitized. Found 100 users of 100 limit.
Checking LDAP ... Finished
Checking GitLab App ...
Git configured correctly? ... yes
Database config exists? ... yes
All migrations up? ... yes
Database contains orphaned GroupMembers? ... no
GitLab config exists? ... yes
GitLab config up to date? ... yes
Log directory writable? ... yes
Tmp directory writable? ... yes
Uploads directory exists? ... yes
Uploads directory has correct permissions? ... yes
Uploads directory tmp has correct permissions? ... yes
Init script exists? ... skipped (omnibus-gitlab has no init script)
Init script up-to-date? ... skipped (omnibus-gitlab has no init script)
Projects have namespace: ...
4/3 ... yes
35/10 ... yes
35/11 ... yes
35/12 ... yes
35/13 ... yes
35/14 ... yes
35/15 ... yes
35/16 ... yes
48/18 ... yes
35/19 ... yes
50/24 ... yes
4/26 ... yes
48/30 ... yes
48/31 ... yes
35/32 ... yes
48/33 ... yes
48/34 ... yes
50/35 ... yes
35/36 ... yes
51/38 ... yes
51/39 ... yes
4/40 ... yes
48/42 ... yes
51/43 ... yes
51/44 ... yes
35/45 ... yes
48/46 ... yes
48/48 ... yes
48/49 ... yes
48/56 ... yes
48/57 ... yes
51/58 ... yes
48/59 ... yes
48/60 ... yes
48/61 ... yes
48/62 ... yes
48/63 ... yes
48/65 ... yes
48/66 ... yes
48/67 ... yes
27/70 ... yes
27/71 ... yes
24/72 ... yes
27/73 ... yes
91/74 ... yes
48/75 ... yes
50/78 ... yes
27/79 ... yes
91/80 ... yes
27/81 ... yes
34/83 ... yes
5/84 ... yes
27/86 ... yes
50/87 ... yes
48/88 ... yes
91/90 ... yes
50/98 ... yes
50/99 ... yes
50/100 ... yes
27/101 ... yes
31/102 ... yes
27/105 ... yes
27/108 ... yes
48/110 ... yes
48/111 ... yes
48/113 ... yes
48/114 ... yes
50/115 ... yes
27/116 ... yes
48/117 ... yes
27/119 ... yes
48/120 ... yes
27/121 ... yes
50/122 ... yes
50/123 ... yes
50/124 ... yes
27/127 ... yes
48/128 ... yes
48/129 ... yes
91/130 ... yes
91/131 ... yes
48/132 ... yes
48/133 ... yes
91/135 ... yes
48/136 ... yes
4/137 ... yes
20/138 ... yes
48/142 ... yes
59/145 ... yes
62/146 ... yes
62/147 ... yes
43/151 ... yes
25/152 ... yes
27/154 ... yes
62/155 ... yes
48/156 ... yes
48/157 ... yes
27/158 ... yes
62/159 ... yes
61/160 ... yes
59/161 ... yes
19/162 ... yes
71/164 ... yes
71/165 ... yes
71/166 ... yes
71/167 ... yes
70/168 ... yes
76/169 ... yes
48/170 ... yes
78/172 ... yes
78/173 ... yes
78/174 ... yes
76/175 ... yes
76/176 ... yes
81/177 ... yes
81/178 ... yes
91/179 ... yes
71/180 ... yes
71/184 ... yes
16/185 ... yes
48/186 ... yes
71/187 ... yes
70/188 ... yes
27/190 ... yes
43/191 ... yes
71/192 ... yes
71/193 ... yes
71/194 ... yes
71/195 ... yes
59/196 ... yes
59/197 ... yes
59/198 ... yes
59/199 ... yes
81/200 ... yes
50/201 ... yes
59/203 ... yes
59/204 ... yes
71/205 ... yes
59/206 ... yes
59/207 ... yes
48/208 ... yes
59/209 ... yes
48/210 ... yes
59/212 ... yes
48/213 ... yes
81/215 ... yes
27/216 ... yes
99/217 ... yes
99/218 ... yes
99/219 ... yes
99/220 ... yes
104/222 ... yes
99/223 ... yes
99/224 ... yes
99/225 ... yes
84/226 ... yes
99/227 ... yes
62/228 ... yes
99/229 ... yes
48/230 ... yes
50/231 ... yes
91/233 ... yes
31/234 ... yes
27/235 ... yes
107/236 ... yes
91/237 ... yes
27/238 ... yes
48/239 ... yes
76/241 ... yes
27/242 ... yes
70/243 ... yes
62/244 ... yes
16/245 ... yes
Redis version >= 5.0.0? ... yes
Ruby version >= 2.7.2 ? ... yes (2.7.2)
Git version >= 2.31.0 ? ... yes (2.31.1)
Git user has default SSH configuration? ... yes
Active users: ... 62
Is authorized keys file accessible? ... yes
GitLab configured to store new projects in hashed storage? ... yes
All projects are in hashed storage? ... yes
Checking GitLab App ... Finished
Checking GitLab subtasks ... Finished